The rep system was actually vastly simplified with v3 of the site, Don. The previous "Fame" system caused constant shortages of service so we had to scrap it. It was just too advanced for our host.
Right now, you gain rep for earning some badges, and if people like your posts they can give you positive rep.
There are timer limits to it, and abuse limits in place as well. All in all it's a pretty relaxed system, and you should be glad if you're in the positives. The folks with 100+ rep have been here for a while, earned tons of badges and made many badass posts. Hence high rep.
You'll see a few people with -X rep, these are usually horrible members who nobody takes seriously. Occasionally they may also be victims of reputation abuse, in which case their rep is reset if it's reported.
It's a swag number, you can't do anything with it, but the more you have, then clearly the more you've been contributing to the site.