Depending on what level you are, you might want to hold off on buying some for a while. Here's some good guidelines for where to start, though:
Marks - Desolation and Insight are great places to start building your mark collection. Desolation gives you armor penetration and Insight gives you magic penetration. Armor penetration is good on anyone who uses their auto-attack, as it's useful for both slower, big hitters and those who want many to do apply-on-hit-effect hits. Magic penetration is useful to help your abilities pierce through any magic resist. There's not many characters that wouldn't benefit from at least one of these and many cast benefit from either.
Seals - Since the removal of dodge runes Flat armour runes are preferable for among other things jungling and supporting. Mana regeneration per level runes are a must have choice for most casters who will be spamming spells often.
Glyphs - Glyphs are tougher to define a good base set for. Celerity is probably the most all-around useful, as it provides cooldown reduction. I don't know of any character who doesn't benefit from that! Shield is an okay choice, as magic resist is useful against most characters, but I prefer the cooldown reduction.
Quintessences - Fortitude is the best all around quintessence, as it makes the early game much easier. When you have 3 Greater Quintessences of Fortitude, you start with +78 health -- that's quite the cushion in the first few levels! Once you have access to the Greater runes (level 30), Wisdom and Evasion become viable choices. 3 Greater Quintessences of Wisdom, along with the Awareness mastery net you 11% more experience and if you're Zilean, you have an extra 8% on top of that. This will give you a noticeable advantage at the end at the sacrifice of the end-game -- unless you can get yourself fed with your higher levels. Swiftness is also a good all-around, as movement speed is always part of the game.
I recommend getting a full book for one character while you're still gaining your summoner levels. This will allow you to rock out at your main character and get used to the game. Once you have a full book, you can branch out into other characters and rune setups. Read up on runes on sites like Solomid and the League of Legends Wikia Wiki.
One last tip: always buy primary runes. When you're buying your first few tier 1 runes, it's okay to go secondary on a few, but don't waste your IP on second-rate runes in tier 2 and tier 3.
If you decide you don't want a certain rune, you can combine several runes to get a new rune. Combining three will net a rune of equal tier and combining five will give you a rune from the next tier up. Other than that, they just kind of hang out in your rune book staging area