There is a thread in the new player section centered entirely on runes, while the mastery questions has been addressed multiple times.
Runes: I use similar runes (m-pen, mana regen, health) on most of my champs, but have enough to have some crit chance or CDR or ability power depending on who j plan on using. It is best to change your masteries once your character has been selected (right before the game actually begins) unfortunately that means that you need to know your role before the game starts)
Most people use the 9-0-21, 0-9-21, 21-0-9, etc etc mastery set up. For example, for my AP champs, I use 9-0-21. This means 9 in offensive (because I want the "your abilities Penetrate 15% of target's MR) and 21 in utility because I want mana regen, exp, and things like clarity and port or clairvoyance.
The masteries you should use vary greatly depending on champ, role, and summoner abilities. (which do you use and we can offer suggestions)