Lately I've tried to use everyone in all the games. FFVI is great for this on multiple playthroughs because there's just so many of them, and learning to exploit the strengths of ones you didn't before is a fun experience.

In FFVIII, I always defaulted to Squall, Zell, and Irvine b/c their limit breaks were just so powerful, but in my last game I set up the girls so they could be powerhouses as well.