I had a thread called "mastering masteries" at one point that analyzed the value of various masteries and laid out some possibilities.
The "default" Mastery build is 9/0/21. In offense, go Crit Damage at level 1 (with 1 point in a summoner skill mastery if you have exhaust/smite, or 1 point in Archmage's savvy if you don't), Cooldown Reduction at level 2, and Archaic Knowledge (Spell penetration) at level 3. Archaic Knowledge is just super good. Even on champions with only a single magic damage skill (Yi's Alpha Strike, Ashe's Arrow), it provides a quite good amount of damage increase. In utility, go increased regeneration at level 1 (again with 1 point in a summoner skill if you've got it or dump the point in good hands otherwise). At level 2, get increased Exp. At level 3, get Meditation (MP/5) and Utility mastery (increased neutral buff duration), and you can put a point in greed if you really want (it's not great, but if you're not using another summoner spell like flash, clairvoyance, or clarity, you may as well). Level 4, get the movespeed, level 5 get cooldown, and cap off with the level 6 for faster summoner spell cooldown.
The only other marginally acceptable builds are 21/9/0 (mostly for improved Rally and the Dodge mastery) or 9/21/0 (for added survivability). The first is only great on Sivir and Katarina, and the second is decent on tanks.
As for runes, here are the generally accepted "best" options:
Marks (offense): Armor Penetration for physically-based heroes, Magic Penetration for magically-based heroes (most tanks do magic damage). These provide more damage per attack/ability than any other option.
Glyphs: Flat Cooldown reduction. This gives ~6%, which combined with a 9/0/21 Mastery set up gives a nice, round, 15%. This allows easily hitting the cap of 40% through 25% effects (Golem, Nashor's Tooth, Frozen Heart, Stacked Mejai's/Deathfire + Blue Potion/Haunting Guise)
Seals: Dodge, HP/Level, MR/Level, or MP/5 (flat or Per level)
Quintessences: Flat HP gives early-game survivability. Alternately, you could buff your lategame by adding a penetration (for offensive types), dodge, or a per level defense.