I play Mages the most and have tried most of the reasonable setups.
What can work in general
Marks: magic pen
Seals: flat mp5 or scaling mp5 (or some combination), flat armor, scaling health, scaling ability power
Glyphs: scaling ap or flat ap, magic pen, scaling mp5, flat cdr, flat magic resist
Quints: flat ap, flat health, magic pen
Explanation: For reds you always want Magic Pen, pretty much no alternative here, nothing else provides as much damage increase for the slot. For seals you pick to make up for an area you're weak in. Mp5 of some kind is always ok for seals, armor if you're scared of losing vs an ad champ in lane and if you, for some reason, aren't worried about any of those take ap/level (usually not worth it). Then for glyphs you usually want to increase your damage output overall with these. Magic pen aren't the best option for mages damage-wise. CDR glyphs are useful, but if you get the 9% from masteries and some from blue pot and potentially blue buff you may create overkill of cdr (max 40%). If you aren't getting cdr elsewhere then they are definitely useful. Also, quite a few people recommend CDR/lvl runes because they help you hit the 40% cap nicely with certain builds, but they often create scenarios where you have too much cdr or you would've preferred to have the flat benefit early. As for the choice between Ap/lvl and flat Ap, it depends on when you want to do more damage. Flat Ap will be stronger before level 6, while Ap/lvl will be equivalent/better at and past level 6. So wherever you want your damage increase is up to you. A last alternative useful glyph is flat magic resist, these will make sure you aren't destroyed by another mage in a 1v1 scenario (kinda situational). Quints are pretty much between Flat Ap and Flat Health. If you are newer to the game, I recommend Flat Health. They will make your mistakes in lane matter less as you have more health to work with. Once you become more skilled Flat Ap are fairly essential because you can usually avoid harassment while dishing out your own more potent harassment.
Personally I run this setup on most mages:
Ap per level