A while back (about a year ago, I think) we had a big mathematical discussion on the board about how saves in general were broken. The consensus by the end was that saves overall were fine, except where someone was of a class that could easily max out one save (Rogues for Reflex, Clerics or Druids for Will) by pumping up one stat. With those classes it was too easy to become effectively immune to one entire type of save.
We came up with a solution: make each save depend on two stats.
Fortitude save is (STR bonus + CON bonus)/2, rounded up. Your ability to resist effects like paralysis, exhaustion, and poison has just as much to do with muscle (STR) as it does the ability to take damage (CON).
Reflex save is (DEX bonus + INT bonus)/2, rounded up. Fast reactions (DEX) allow you to dodge the blast before it reaches you; but the ability to process information (INT) allows you to figure out quickly where the blast is going to be aimed (and therefore which direction gives the best chance of escape).
Will save is (WIS bonus + CHA bonus)/2, rounded up. When dealing with mind-affecting spells, your sense of self (CHA) is just as important as your ability to realize that something is wrong (WIS).
End result: for those classes that need multiple stats, your saves don't change much. Wizards gain a little Reflex save, Sorcerers gain a little Will save (which helps differentiate the two). Clerics, Rogues, and Druids lose a bit. Oh, and CHA stops being such a dump stat; it and WIS are still relatively weaker than the other stats, but no one can entirely dump one.
Also, items/Feats that increase one save directly become a little stronger, while those that increase CON, WIS, or DEX become a little weaker.
Ironically, by making STR an even stronger stat, the Half-Orcs don't suck as badly. Well, that and I let them take Limited Scent as a Feat (it's Scent but at 1/3 the range and +5 to DCs)