The D&D game I'm playing in is pretty fun because we've experimented with all kinds of races and classes. Almost the entire Complete series of alternate core classes has been touched on, as well as classes from several other sources. We used races from the Races of... series, including my two characters which were Eberron races (changeling and shifter.)
In the last game I ran, I used all kinds of alternate rules, but they weren't just options; they actually replaced several key core rules. I had alternate classes, action points, armor converting damage to subdual damage, sanity, and all kinds of other rules, and I think it all held together very well.
Another rule that makes so much sense that it should be default is fractional BAB and saving throws. It's particularly important in d20 Modern where multiclassing is more common, but even in D&D I think there's no reason not to use this rule.