I've read a lot of different things about that, but I don't keep links. :/
I suggest checking out the Wikipedia article on "humans", under the section "diet", I found a few good links from there (although several are to papers, not Web sites). There is correlation between certain types of cancer and meat intake (and we all know that correlation implies causation (just kidding!)).
Also, keep in mind environmental issues. I don't have a link handy, but the meat industry is the highest producer of greenhouse gases, and disposing of the "solid waste" from farms has become a serious issue. Groundwater/runoff contamination, among other things, are destroying the farmland. Not to mention it takes at least 10x more land to raise cattle compared to vegetables, for the same amount of caloric intake.
Part of that goes back to the Tragedy of the Commons, which is something I recommend reading for this essay. Sure, animals can be grown in a way that doesn't destroy the land, but if Farmer A does that, and farmers B through Z use the way that destroys the land and they raise 10x as many cattle for cheaper, Farmer A is going to be in the welfare line. Same goes for vegetable production, with pesticides and stuff, but cattle are much worse.
Another danger is that livestock are given a lot of chemicals, like unnecessary antibiotics, growth steroids, etc. Unnecessary antibiotics in livestock, like humans, leads to antibiotic-resistant strains of bacteria, creating a need for stronger antibiotics. That's a cycle that we're eventually going to lose. Also, the chemicals fed to cows almost certainly make it into the meat that people eat.
One of the main arguments against vegetarianism/veganism is that we don't get enough vitamins/minerals. That is, of course, nonsense. The Canadian Foodguide (and I'm sure the American Foodguide as well, or whatever you call it) says that a well-planned vegan or vegetarian diet can provide all required nutrients and lower the risk of heart disease and cancer. That's almost a direct quote from a pamphlet I lose. Another argument against it is that vegetarians/vegans are always hungry, but that's not true either -- if you get enough protein and fat, you'll feel full.
Then there's always the the cruelty side. Babies taken away from their parents when they're born, and killed outright if they're useless (ie, male cows aren't kept because they can't produce milk). Babies are fed nutritional supplements and kept in cages, away from their parents. Chickens are often debeaked, which is arguably a painful process. Animals are frequently abused/killed. It's not a fun time for them.
Those are the arguments that come to mind first and foremost. You will, of course, have to find proper studies/articles to reference, which I'm afraid I can't help you with. That's funny, because it's what you asked for -- sorry about that.
But I think the above arguments are the main ones that vegetarians/vegans use.
Also, I'd be interested in at least seeing your bibliography, or even seeing your full paper if you don't mind.
