Both are still important. Masteries give a boost late game, runes give early game stats (rule of thumb).
http://forums.na.leagueoflegends.com/board/showthread.php?t=4418901
^Rune efficiency table and a few thoughts on runes that are good.
http://boards.na.leagueoflegends.com/en/c/tips-tricks/9I8KcQGh-runes-418?comment=00010000
^Specific list of runes that are strong atm
Masteries are usually set up as 21/9/0 (assassins) 21/0/9 (mages) 25/5/0 (a few hybrid assassins) 9/21/0 (most tanks) 21/9/0 (adcs) 0/13/17 (most supports).
Double edged sword is a great mastery for melees, okay for ranged. Dangerous game is really good, spell weaving/bladeweaving depend on your champ. Rest of offensive masteries are self-explanatory.
Block/unyielding are super strong on laners. Enchanted armor is super important on tanks. Tough skin is only for junglers, dont take it as a laner. Juggernaut is really really good, oppression can be good dependign on your champ. If going 21 into defense, take 8 points tiers 1/2 in whatever makes sense for your role, hardiness, oppression if your champ has soft cc. Perseverance is quite good. Only take second wind if you have lots of heals, reinforced armor can be a good option. Swiftness can be useful if you're worried about being kited. Legendary guardian is SUPER strong, but you don't have to take all 4 points. Tenacious can be good. The only big no-no is runic blessing, NEVER take that.
Utility masteries are pretty bleh. If you're taking 9 points, your tier 1 choices dont matter too much. Just don't take scout and you're fine. In tier 2 take summoner's insight and alchemist. Runic affinity is still really good, but if you dont need blue/red, culinary master can be good. Just an fyi, pop your pots 1 at a time if you take that; its bonus won't work if you queue your pots up. If you're putting 17 points in utility, take gp/10 at tier 3, wealth and scavenger at tier 4. The last 2 points required in tier 4 don't matter too much, but bandit is super super strong as a ranged support. it's not often worth going 21 points into utility, the only possible exception is ryze (for increased mana pool and cdr)