First off, a note of caution that all of this applies only to how your imported single-player game will interact with your ME3 single-player game. Multiplayer games obviously make game companies a bit touchy about people changing the game balance, and both Microsoft and EA can, have and will ban people for modding. A modded ME2 import shouldn't make a difference to this, because there's no real reason for the multiplayer servers to even be looking at your single-player save games. But these are the people who gave us Origin, so there's no guarantee they won't look regardless (by the way, you're all using Sandboxie to keep Origin from poking its nose where it doesn't belong, yes?), so if multiplayer and/or your Xbox live account is important to you, you may want to hold off on importing any modded Shepards until we've had a chance to test the waters and see how it goes.
Now, back to the main post!
So let's get this out of the way: BioWare employees themselves have a scripted answer to the question "will my mods break my game." It sounds really ominious and scary and seems custom-designed to make you freak the fuck out and restart your game from scratch just to be safe, so I'm not even going to repeat it here, I'm going to give you the translation instead. BioWare's official position is this:
"If you don't use your game as we intended, we can't guarantee it will work as we intended."
That's not only perfectly reasonable and not-at-all-ominous, it's even actually a good thing. If you're modding your game, you don't want it to work as they intended in the first place! For example, they intend you to only get to choose from six different skin tones. I have modded around that limitation. I would be extremely put out if somehow all my Sheps got reverted to those six intended skintones in ME3; I want my Sheps to continue to work not as intended.
And that leads us into the first category of mods!
There are two kinds of aesthetic mods in Mass Effect. The first kind are what we call TexMods. They use a third-party program, called TexMod, to swap ingame textures for other textures.
TexMods are 100% import-safe, because the game doesn't even know they exist. TexMod functions by interfering with your graphics driver. Basically when the game tells the graphics driver "look up this texture," TexMod goes "hey wait! Use this one instead," and your graphics driver obediently does. That can't affect your ME3 game because it's not even in your ME2 game.
Now, TexMods may not "import" properly, in the sense that if you change the texture of Shepard's shirt, and then ME3 uses a different name for that texture than ME2 did, TexMod won't know to intercept it. Fortunately that takes like four seconds to fix, so TexModders will take care of it pretty quickly post-launch and you just have to wait for the updates.
The second kind of mods are done with Gibbed, and involve editing your Shepard's head by changing eye or skin color, replacing one hair type with another, or swapping out one of the male Shepard complexions for Sheploo's or your eyes for the Illusive Man's glowy ones, or similar adjustments.
These work because of the way the game stores information about your Shepard's head. Each "complexion" Shepard can have is a fixed texture; each hairstyle is a pre-defined mesh; each color is just a set of RGB values. When it goes to render your head in the game, it looks at the data for your particular head shape and says "ok, this one says it uses the Classy haircut and the Freckles texture," and then goes into a file somewhere and looks up what the Classy haircut and Freckles texture look like. When it goes to render your hair color, it just paints over that hair mesh it just loaded with the colors indicated by the RGB values.
So when you change your hair to use Nef's "sexy" style or Kelly's "mom" style, all you're doing is telling it to look somewhere else for the hair. If you change your eye color, all you're telling it to do is paint your eyes with a different amount of red, blue and green. What this means is that if you're using Kelly's hair, as long as Kelly is still in the game in ME3 (she is), and her hair mesh still has the same filename in the same file structure, your hair will import perfectly. And they won't change the file structure, because if they did, they'd break the import of all the hairs, including the legit ones. On the 0.1% chance that they do change the file name, the game will try to load a hair mesh that isn't there, and your Shepard will just be bald. You'll be able to fix that in Gibbed as soon as we find the new filename, which again, shouldn't take us long.
Same goes for TIM's eyes - he's still in the game, those textures will still be there. The worst that will happen is they get moved and your eyes display with solid black irises because there's no texture until we find their new location. Color is even safer; the colors are just numbers in the file, the game's not checking them against anything, it's using them on the fly.
Clothing, Armor and Equipment - C.ini editing
Another mod we think of as "aesthetic" is the wardrobe or locker mod, which allows you to choose for your casual clothing any clothing in the game. It may also allow you to wear Shep's old ME1 N7 armor, or use different colors for your armor than the limited base selection.
This kind of mod actually falls into the same category as mods that let you skip or fast-forward through the intro movies, equip different weapons to yourself or your squadmates, separate the Storm and Use keys, make the Hammerhead not quite so made of tissue paper, alter the damage of guns, change the health modifiers for different difficulty levels, add a screencap keybind, make the Locust carry over into NG+, and unlock the Claymore for your whole squad when you pick it up on the Collector Ship, among other things. They all work the same way - by modifying Coalesced.ini, a game file that governs the way ME2 reads and uses the rest of its files.
Like TexMod files, these mods are 100% import-safe, because they don't actually touch your save game. ME3 doesn't care what ME2 is doing, it only cares what your save game says, and C.ini mods have no impact whatsoever on your save game; they only change what ME2 itself does with the information in it. However, also like TexMod, they therefore won't import into ME3.
ME1 Decisions and Other Plot Flags
The last common form of modding is to use the Gibbed editor to alter your Shepard's plot decisions and resources. Starting the game with 10000 points each of Paragon and Renegade so you can roleplay more freely, or giving yourself a zillion platinum so you don't have to mine, or starting a new ME2 Shepard but still giving her a history with Gianna Parisini and sparing the Rachni Queen and romancing one of the ME1 LIs. With the most recent eddition of Gibbed there's also been some editing of ME2 plot flags, like removing character loyalty to generate a specific Suicide Mission outcome, or fixing the Conrad Verner bug, or recruiting certain characters early.
The impact this kind of modding will have on ME3 importing is a matter of degree. See, the ME2 import from ME1 was relatively unsophisticated, and we have no reason to believe ME3 will be different, and good reason to believe it will be the same, because it doesn't need to be very sophisticated. All it needs to know to work perfectly with any normal, unmodded game is things like "did you recruit X. Did you romance X. Did you kill X. Did you have Y conversation. Did you collect Y codex entry." It's also going to check some basic integers: "how many points of paragon, how much money, what xp value/character level, how many points in this class power." It's just going to read your game, as-is, and look for certain values in certain places.
What this means: the game doesn't care how you got those points or that money or that character's loyalty. It's also not going to care when you did that recruitment or advanced that conversation. So if you did very simple things, like increase integers (give yourself more money/resources/morality points/experience points), or did things out of order (picked up Tali first, set an ME1 romance active halfway through Horizon), it won't matter. Anything you do that you could have achieved in a legitimate way, you might as well have done legitimately, as far as the import process is concerned.
If you do things that you couldn't have done legitimately, things get slightly less reliable. One possibility is to have two conflicting flags. If you, for whatever reason, tell the game you both spared the Rachni Queen and killed the Rachni Queen, there is a slim possibility your game will lock up. But I do mean slim. When you're a programmer and you have a script to put together that differs based on two mutually exclusive outcomes, you don't check for both. You check for one of them, and if it's true, you don't bother to check for the other, because you know that it's false. If it's false, you still don't bother to check for the other, because you know that it's true. So whichever the game checks for first, it will use.
This could cause pretty strange behavior if one scene checks "is queen dead? ok do this" first, and another scene checks "is queen alive? ok do this" first instead. It might wreak havoc with your Galactic Readiness Score and do strange things to the plot, or cause characters to show up when they shouldn't or not show up when they should. It still probably won't lock up your game, because the game engine appears to have pretty good fallback mechanisms for allowing conversations and cutscenes to continue when audio files are missing or characters aren't present. But I advise against testing it out: when you alter plot flags, always make sure they don't contradict each other.
Another possibility for doing things you couldn't do legitimately is accessing content that's legit for some players, but normally locked out for your character type. This could mean giving yourself the "unlocked the Widow" flag on a sentinel, but the most common example is those of us who hacked our games to romance Ashley/Miranda/Tali/Jack with femShep or Kaidan/Garrus/Thane/Jacob with dudeShep.
The thing here is that the game knows how to do what you're asking it to do. It has provisions for "Shepard in a romance with character X." It has dialog, and cutscenes, and if there are places where there's some equation for successful negotiation where "in a romance" is a factor, it's going to calculate those accuately - because again, if you're coding, you check for "romance" flag, not "romance plus correct gender" flag, because if the game is playing as you intended as a developer, correct gender is guaranteed by the romance flag to begin with, so why waste time and bits on extra conditions?
But the resources to execute those results might not always exist. For example, if you romance your s/s Virmire Survivor, the confrontation on Horizon will play out perfectly. Meer and Hale recorded all of each other's lines, and those lines were put in the right places in the game files, so when the dialog system gets to those responses it just plays the correct audio file for "romance flag response" out of the correct set of folders for "Shep gender" and everything's fine. But in the conversation with Joker afterward, the paragon response for Kaidan is only voiced by Hale, and the one for Ashley is only voiced by Meer. The romance dialogs for ME2 are all unvoiced for s/s as well. So what happens if you select those lines?
Well, nothing dramatic. Your game doesn't crash or explode. Like I said above, there are fallback mechanisms for when audio is missing, so the game just plays a few seconds of silence, displays the correct subtitles, and the conversation continues on. Your Shepard goes through the right animations, because those aren't gender-dependent. The right conversation flags get set and things advance exactly as they would for the "proper" gender of Shepard. Just, without voiceover. It's a little annoying, but that's it.
The only possible conflict I can see here that would really bork things up is if Ash and Kaidan turn out to be legit romanceable for s/s in ME3, which is looking reasonably likely. If so, I'd expect the new romance dialog would check first for "active romance with VS," and then only if that flag were absent would it trip the new dialog. But if any of the new dialog is particularly gendered, it might simply check for "femShep/dudeShep" on the assumption that that automatically includes "no active romance with Ashley/Kaidan." In which case you could see the problem I described above, where some lines or conversations assume an active relationship and others behave as though there's none. Again, this is really, really unlikely to actually kill your game or make it at all unplayable. It's not even likely to actually happen. But this is one case where the slim possibility does exist. Fortunately, it's as easy to fix as opening your save with Gibbed and unchecking the romance flag for the VS in question. You can't easily do this with the ME2 LIs, but they will definitely not have any conflicting romance in ME3, so it's not an issue with them anyway.
Basically, your game is 99.9% likely to be fine if you don't go out of your way to intentionally set up plot outcomes that would be impossible for any Shepard to ever achieve. The only real concern is the mild possibility of distracting but harmless problems like silent dialog or missing hair meshes. And on the 0.1% chance that something does go seriously wrong, fixing will be as easy as opening your ME2 save with Gibbed and removing whatever flag is causing the conflict.
So there you go. You may now mod and import with confidence. :)