The very first paragraph of Thomson's site reads as follows:
"This site's purpose is to give you the means to contact Miami attorney Jack Thompson if you know of someone harmed as a result of violent entertainment, including violent video games."
There appears to be no room for discussion; he's created causality (video games leads to violence) with no verifiable proof. As a lawyer, he doesn't need to, and all he really relies on is anecdotal evidence in the form of a client looking to sue on behalf of game consumers.
I wouldn't mind if he took up this cause after major research studies show that, for instance, heavy gamers are 50% more likely to react to stressful situations with violence. That would be a damning indictment of games, don't you think? The problem is that this kind of research simply does not exist.
I'd love to get my hands on some of the money from the CAMRA Act (google it, or check thomas.loc.gov) to do some research on games and children, and good thing the appropriations don't begin until 2006. Something like this could serve as a fantastic post-dissertation project. My first book, perhaps? I could write about games until the

in' cows come home.
In the meantime, there's not much to debate about Thomson. He believes he's right, and as a lawyer, he's free to make that claim and cash his lawyer checks. Most gamers believe that he's undoubtedly wrong, and that games don't have any negative effect on people whatsoever.
I happen to have the only opinion out there that borders on truth: we don't know shit. These studies haven't been done in depth, and even if we do, the demographics keep changing, circumstances keep changing, etc.; researchers need to get off their ass to do this kind of work.
For instance, at a conference in April, I saw a

ing tenured professor present "research'' on WoW. I say "research" because it is evident that he wasted his entire Winter break playing WoW instead of writing something substantive about the game. I came up severely disappointed in the presentation, but I jotted down about a dozen highly important topics that stem from the social world of MMORPGs: off the top o' my head, a few were:
1) Gender Roles: (56% of characters were female, and the professor claimed that 80% of players were male when I asked, and I personally believe it is higher than that)
2) Division of Labor: People who "specialize" in MMORPGs, such as Cantina Musicians in Star Wars Galaxies. It seems more like labor than a game, does that not?
3) Economics: Some people make a

ton of real-life money selling virtual goods online
4) Racial Profiling: There are stereotypes that those people in #3 are all of some Asian ethnic group
5) Crime (My Favorite): It's somewhat common knowledge that a woman, upset that her boyfriend split up with her, deleted his MMORPG account for a game called Lineage. Now, she was later arrested for theft/destruction of property. Combined with #3, in the future people could be potentially charged with felonies for this kind of behavior.
There are other ideas in my "to do never" folder; however, I think that looking into the effects of games is excellent, and given its popularity, a necessity. However, the approach Jack Thomson takes is wrong and logically flawed; this does not mean, on the contrary, that a reactionary approach to Thomson's rhetoric (games don't effect people!) is any more correct.