Some runes for stats are more efficient in some slots than others. For AP runes, I'd recommend flat AP quints, flat AP glyphs, and scaling AP glyphs as the best options.
Generally, I have three pages for AP champions:
- [General] AP Quints, Armor Seals, Flat MR Glyphs, Hybrid/Magic Pen Marks
- [vs AD] AP Quints, Armor Seals, Scaling CDR Glyphs, Hybrid/Magic Pen Marks
- [vs AP] AP Quints, Scaling Health Seals, Flat MR Glyphs, Hybrid/Magic Pen Marks
Health runes are nice when you are against mixed damage and need additional durability.
I wouldn't recommend using mana regen runes, but if you insist then they are good when a champion spams spells a lot but you can't really afford to build much mana or mana regeneration. Typically, intelligent mana use and Doran's Ring(s)/Crystalline Flask is enough to sustain you.