I think that for your own sanity, as GM, that you should limit the player's PC to magic that is defined in the setting, whether published or homebrew, unless and until you feel comfortable expanding the options to include an alternative source.
For Iron Kingdoms, I would say "You are limitted to the way magic works in this setting, but you may design a Sight spell, provided that I approve of it." I then put the onus of work on the player to write up the spell description in the same format as in the relevant book, and then I have to approve it, possibly with revisions. I reserve the right to reject a spell either on balance issues or on setting issues.
(For example, I've rejected two spells. One was too powerful for its spell level. The other was a divine spell which I thought the character's deity would choose not to grant, even though it was a pretty cool spell and nicely balanced.)
In fact, for Runequest I would encourage the players to design their own spells. (This is also encouraged in the IK setting, which says that "sorcerers" especially should be encouraged to design their own spells.) But the GM really has to stay on top of this to prevent abuse.
As to alternative magics: one strength of Runequest is the way that alternative magic systems can easily be implemented. If you have not gotten the Runequest Companion book yet, I highly recommend it, since it defines two alternatives to the Runecasting system presented in the MRQ rulebook. Importing a magic system from another game system is doable and can really add a lot of flavor to your campaign.
As for a comprehensive list of skills, I'm afraid that we can not do that. The possibilities are really as endless as your imagination.
