I think most aftermarket panniers require a different rack than stock (exception is the Brooks panniers). Most other racks will use a flat profile so you can mix and match one style rack with many different panniers. However, the quick and dirty approach is to just buy the same brand pannier and rack. Most are $250-$500 for the racks.
I put the SW-Motech racks on my GS (I like the camlock release mechanism for quick removal of the entire rack and pannier) and on these I can mount Givi, Pelican, Jesse, H&B, Happy Trails, Tusk, homebrew, etc.
Pro's and con's to whichever approach you take.