I've never liked the way Mythos Magic was handled in GURPSCthulhupunk. I didn't like its "Mythos Fright Check", and rolling one every time you cast a spell sounds unwieldy. However, after reading through GURPSFantasy, I think I have come up with a good alternative.

Every time someone casts a Mythos spell, it not only costs fatigue, but the expended energy also goes towards a "point debt" that accumulates with each cast spell. Every time the debt reaches a certain limit (25, 50, or 2dx5 might all be appropriate, depending on your campaign), it is erased and exchanged with a 5 point disadvantage or it worsens an existing disadvantage by 5 points. It's probably best to start with mental disadvantages, but later on - or if the character has been busy casting some of the nastier spells - appropriately gruesome physical disadvantages are certainly in order.

If you feel generous, the point debt might decrease naturally over time - one point per week or one point per month might both work. This allows the characters to use magic in care cases and emergencies without siginificant problems. Naturally, you shouldn't tell the players how fast (if at all) their debt is reduced, or how high the threshold is - just take the relevant player aside at an appropriate moment and tell him about the new problem he has developed...

Certain mystics and mages might have developed meditative techniques that reduce the debt at a faster rate (such as one point per day of meditation), but that is probably something best left to NPCs in modern-era Cthulhu campaigns.