One of the things that annoys me most about this is that **** like this make it really difficult to criticize her work. A lot of her stuff is really dishonest, but it doesn't matter because she's the victim of a lot of harassment. The legitimate critics either go unheard, or they're demonized and lumped in with the morons.
I've seen accusations of dishonesty flung about freely regarding the TvW videos, but I've never seen a sane person come up with sane explanations. It's all "Game <x> was misrepresented!" or "This scene was taken out of context!", which to me sounds more like people desperate to justify their particular tastes than good, factual critique.
I've also not seen a good refutation of the overall point Sarkeesian makes (that being that representation of women in games is deeply problematic due to it falling in a narrow range of stereotypes).
I would like to see both of those things though; After all, any hypothesis is only as strong as the criticism it can withstand.
I don't actually disagree with Sarkeesian's premise, but I actually do think it matters what examples she uses. The recent Hitman one is a great case, actually.
Basically, part of a mission in Hitman: Absolution goes through a stripclub. Naturally, this being Hitman, you have the ability to kill pretty much anyone you want, which includes the strippers. But, since they're innocents, you're penalized for doing so. Sarkeesian uses this as an example of sexism, treating it as though that was the whole point of the game, that "the player cannot help but treat these female bodies as things to be acted upon, because they were designed, constructed and placed in the environment for that singular purpose. Players are meant to derive a perverse pleasure from desecrating the bodies of unsuspecting virtual female characters." All the while using footage of the player dragging the bodies around in a great big circle to show just how objectified and disposable these women are.
Not only is this them being treated like every single other npc in the game, be they male or female, but she says earlier in the video (generally speaking) "...this kind of misogynistic behavior isn't always mandatory; often it's player-directed, but it is always implicitly encouraged." which is crap, given that, again, Hitman penalises you for killing innocents, and in that specific case, they're actually out of your way. It's like she takes the mere existence of vulnerable female characters as encouragement to harm them.
What is that if not misrepresentation? It's completely dishonest. There are plenty of good examples to make her point, some of which she uses herself (the Mass Effect one in particular), so why is this kind of dishonesty even necessary?
The video is
here, should you want to watch it. Part I'm talking about is at 21:46, but the whole thing is worth watching.
There's also the whole part where she doesn't seem to understand what a background character is, but I'm not talking about that right now.
While I'm on the topic, I noticed a trend with her a while ago: she focuses on the way female characters get treated, whether or not male NPCs in a given game also get treated the same way. Now, she explains that this isn't ok because of a power differential in modern society. Ok, that's fine. What is the solution, then? If a game has female characters, they must be in a position of power or it's sexism? Women can't be vulnerable ever, and a game can't even show sexist situations or it's reinforcing the patriarchy?
Christ, she uses footage from New Vegas (among others) to illustrate this. I don't know if you've played it, but that game is probably as far from sexist as you can get in the modern gaming industry. It depicts sexism (hi Caesar's Legion), but it deals with it quite seriously. I'm not saying that, as a counterexample, this invalidates her premise. It doesn't, but it certainly doesn't support it. I haven't played every game she chooses to talk about, so how do I know she's not doing this elsewhere with other games? Whether it's conscious or not, it undermines her entire methodology, and I rather dislike her for it.
But if there's one question I wish I could ask her, it's this: Can a game depict sexism without being sexist in itself? Can it allow the player to engage in activities that could be considered sexist without being sexist itself? Given the way she deals with her critics, I don't think I'd be likely to get a serious response.
Honestly, I wish I had the patience to go through all her videos and actually write something up. Like I said before, I don't actually disagree with her central premise, but I do have a problem with the way she demonstrates it, and I don't think she deserves most of the praise (or the hate) she gets.
I do hope this qualifies as a sane explanation.

And like Flipside, I used to rather like Thunderf00t's stuff (and his science-related work is still excellent), but I think he's getting a bit too angry about this issue. I've been avoiding his feminism-related videos for a while. His complete and utter lack of tact really doesn't help, given how heated this discussion is in the first place.