so I finished the companions quest and im the harbrigner (I think thats how you spell it) and I also finished the mages guild quest and im the archmage... in oblivion, when I finished the fighters guild quest I got to get paid and tell them what to do, and now I only seem to be able to get them to follow me around, are there any perks im missing here?

Well, the Companions don't really like being told what to do...

what about the college of winterhold?

I don't know; I've never been Archmage.

No real perks for any of the guilds. Get followers from the Companions, you get a bedroom as the Archmage, you get a sanctuary from the DB, and you get more fences around Skyrim for the Thieve's. As for the Civil War, well...you get absolutely nothing.