I have a slightly off-the-wall suggestion: If you want a flexible general-purpose system to introduce more special abilities to a d20 game, you could buy a copy of Mutants & Masterminds 2nd Edition (3rd seems to have moved even further away from the d20 system; since 3rd came out there are many copies of 2nd floating around):
You could, with a little effort, adopt the book's Powers chapter for your game. Powers in M&M are bought with power points that M&M characters get normally. Introduce a new feat:
You have a strange ability that sets you apart, even from other heroes.
Benefit: You receive 5 power points that you may spend on powers from
the Powers chapter of Mutants & Masterminds. The GM must specially approve
your use of this feat. The Power Level for purposes of power acquisition is
equal to your character level.
Normal: Characters in Pathfinder do not normally receive power points.
Special: This feat can be taken multiple times.
Just be aware that you'll have to read the chapter beforehand and decide what you want your players to be permitted to take (your swords & sorcery fantasy game might be severely disrupted by a player with, for example, invulnerability to magic, or the ability to fly at 750 MPH for 16 hours a day).
Also, you'll need to convert some of the powers for d20 use; mostly this would mean converting damage from their wounds system to stock d20's hit points. I'd use the equipment chapter's weapons table for that. Other stuff works the same, such as initiative, ability checks, skill checks, saving throws, attack rolls, and armor class. What counts as Extraordinary, Supernatural, and Spell-Like, I think, would be self-evident, and that handles cases such as "does spell resistance apply?"
It'd be work, but once you were done, you'd really have something flexible and powerful. You can do anything with M&M powers.