Hmm. I can't remember most of the cliques being particularly insular in that fashion that everybody seems to stereotype them as. The Computer Systems Lab, band, two of the [East] Asian cliques (the fobby azn ones), and maybe the weeaboos were probably the only ones that were like that. Most of it was really class consciousness (har) like HistoryBuff said, or geographical, since my high school pulled students from such a wide area; people who shared the same "base" high school tended to be best acquainted with each other in freshman year for obvious reasons.
I mean, obviously, there were groups that you'd hang out with, but they had a helluva lot of overlap and it wasn't particularly hard to insinuate yourself into any given one, even the Group of People Who Actually Did What Most People Claim To Remember Doing In High School. That last group isn't the same thing as "popular kids" (har). Popularity was really kinda weird; we didn't have class rankings, so the student who addressed us at graduation was a guy who was known for being kinda nerdy, extremely goofy, and very funny, and who rode a groundswell of support as an upperclassman to randomly become the most well known and well liked guy in the class.
Of course, the problem arose when people overexaggerated how nerdy people actually were and it got trite. The principal, for instance, and the people who wrote for the school newspaper. According to madviking and a few others, the principal got even more annoying with some of his antics after I graduated; in my senior year, it was mostly limited to riding around in a Segway after school and pulling out a toy lightsaber in his address at graduation.