hawkeyefan
Legend
I have a very simple rule for that: conversing with the GM before/after making the character and leveling up. I expect the same from my players when GMing.
My opinion is that the 3e/PF system is pretty modular. A couple of feats and/or spells per character, or an archetype is not so much a material the GM couldn't keep up with, IMO.
If the specific thing the player want to use uses a specific subsystem my game doesn't using, like for example sanity-specific things from PF's Horror adventures when the game isn't using the sanity rules, in that case it is simply off-limit, because without the additional system the whole thing is moot.
But taking a feat from here, a spell from there, I don't see it as big a problem, especially with the PRD. In the recent 3.5 underdark game I'm playing in i made my character from literally 5 books and the GM had zero problems with that and he's a very casual one, with many other responsibilities and a little child etc. I was just upfront with my character and shared with him where i got this and that from. It's not even a low-level game, we're 7th level without taking into account the more powerful races.
We did plenty of that, and it wasn't a problem at all times, but it was often enough to be an issue. Plus, playtesting isn't retroactive. Pathfinder added all kinds of crazy content as they went along....but their old modules and adventure paths were not designed or playtested with the later options in mind. So it becomes very hard to predict the impact all the new options may have on any older material. I found that to be a particular problem in Pathfinder with classes like the Alchemist and Summoner and Gunslinger. All cool concepts, but really drastically different in design from the core classes.