At the recent Chicago gameday, I was chatting with some folks between games and I think it was KnowTheToe who said that he had spent some time (a lot of time, I'm sure) making a "campaign bible" that included custom core classes, feats, etc. mostly all from OGL sources, but all combined in a single document. I've always wanted to do that.
In general, I think all those "systems" work very well with each other. Of course, there's some specific issues that might crop up, so you have to keep your eyes open, but I mix and match quite a bit myself.