My general thoughts on the issue (And my apologies in advance, as I will likely not add anything new to the discussion, and this will be fairly incoherent as well):
As someone who has recently taken an interest in speed-running games, I must say that some of the time attacks here have helped me greatly, either in refining my own technique (IE "Okay, move A is easy enough to do on a console...all right, move B seems impossible, but let's try move C instead..hey, that'll save me a few seconds..." etc.), or in identifying glitches that should be discussed before a speedrun is attempted (As TwinGalaxies generally frowns on glitches). In short, I personally have no major problems with them, as long as the authors and whoever passes them on are forthcoming about the methods used in recording them (Slowdown, save states, anything else I may have missed).
Now, from what I observed--and I could very well be wrong--most of the controversy concerning these videos ignited when Morimoto's SMB3 video was passed around as, for lack of a better term, a "legit" gaming performance, through no fault of his own (As an amusing sidenote, people seemed determined to discredit the video by any means possible. My personal favorite was "OMG H R TEH CHEATER LOOK AT TEH CLOK CHANGE SPEEDS!!1!", as anyone who's actually paid attention when they play the game knows the game clock is based on Mario's speed). Since then, a primary mantra of the time attack community has been "We don't claim that these are legitimate gaming performances".
Yet from what I've seen, the actions of the community do not always support the words. Now I'll grant that things may have changed recently (The first example in particular is almost a year old). Around February of this year, Arc posted on the Metroid2002 forums (Topic at
http://www.metroid2002.com/forum/viewtopic.php?t=210 and scroll down a bit) saying "Look at my 17-minute run!" and a link to his tool-assisted video. And that was it. It was only after he got called out on it that he A. admitted it was tool-assisted, and B. posted the link to the Why and How page. By then, of course, it was too late; the damage had been done, and the speedrunners vs. time-attackers rift had widened. Now as near as I can tell, Arc had initially expected those who watched it to magically find their way to the Why and How page after watching the video. Of course, most of the people there didn't do this, but I still feel as though Arc should have been a little more forthcoming about his methods initially.
Then, of course, there was the Super Metroid time-attack that someone tried to pass off as a legitimate run sometime in August. As near as I can tell, this was the worst-case scenario brought to life, the situation that speedrunners and timeattackers alike fear (The speedrunners because this compromises everything they do; the timeattackers because it seemingly contradicts their message of "We're not competing with the speedrunners"). Yet from what I read, the basic reaction from this community was little more than "Oh, too bad someone tried to submit it as a legitimate run, because it's a great time attack...". Were I a timeattacker, I would've made sure to distance myself from whoever tried to pass the video off as legit as much as possible, to make it clear that passing emulator-assisted movies off as legitimate runs is not what I nor the community is about. Of course, maybe this was done, and I just didn't see it.
Yet at the same time, I find the primary complaint of speedrunners--that tool-assisted videos somehow take away interest from what they're doing--to be a strange one at best. I personally feel that if you're speedrunning games primarily for some sort of Internet glory, you should really rethink your motives. Nor do I buy the argument that timeattackers are somehow less skilled than speedrunners. I'll grant that making a tool-assisted video requires a very
different skillset (Yeah, you can tell I've hung out at Twin Galaxies) than speedrunning, but the massive investments of time on both sides seems to me to be more similar than either side may want to admit.
Just an outsider's take on the issue.
EDIT: I was evidently in error when I said that it was presumably the author of the Super Metroid video that tried to pass it off as legit. This has been changed, and I apologize for the inaccuracy.