Runes... Let's see...
Anything Lightning/Thunder based from Suikoden II. I loved the lightning effects. Never has lightning looked more deadly in an RPG.
I'm big on Double Beat Runes (Suikoden II). Mainly because they are so easily obtained (and at the beginning of the game!) and so damned fun. No sane monster would randomly encounter my party with this setup:
Killey with a Double Beat Rune, Gale Rune (or the 'Speed' rune, as I like to call it), and a Double Strike Rune. Add to his weapon the rune that makes your attack go up each round (forgot it's name

), and Killey = ownage. If he has Beserk on, it's even more the ownage. Hence my abuse of the Bright Sheild Rune.
The Double Strike Rune is a double edged sword, as it gives the character that attacks with it more attack power, but in return, the enemies also do more damage to whoever has the Double Strike Rune. So I don't really use it much, only on my godlike Killey setup.
Another favorite is the Holy Rune in Suikoden. Makes Mcdohl able to move a hell of a lot faster .
I am more for runes that raise your attacks/stats and not so much the magical runes. I never really used to much magic in the Suikoden games, except against bosses.