How do I choose which Runes to get in League of Legends?

Since runes cost influence points, I'm reluctant to just try getting a bunch of them. Also, as a low level summoner, I am still experimenting with different characters. Are there some guidelines for choosing which ones to get?

If I don't want to use a particular rune, is there anything else I can do with it?

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

While the other answers here do have some decent advice, I think it is important to note the principles behind buying certain runes. First and foremost, it is important to understand the difference between primary runes and secondary runes. Runes are paired by stat and type (e.g. magic penetration marks and magic penetration glyphs), but there is only one rune type which has the maximum stat bonus for each stat. So, for magic penetration, marks are the primary rune because they have 0.95 magic pen per rune, whereas glyphs are secondary because they have 0.57 magic pen per rune (there are no magic pen seals). Quintessences are a breed of their own - they provide more stat boost per run than any other type so all quintessences can effectively be thought of as primary. In general, you want to only buy primary runes, although on certain champions it can be beneficial to purchase other types (such as attack speed on Irelia to boost her passive heal and true damage per hit).

Check out this link for a quick reference of rune stats: http://leagueoflegends.wikia.com/wiki/List_of_runes#Full_Runes_List.

Another basic principle of buying runes (in my opinion) is that they are mostly for getting an advantage over your opponent early in the game. By the end of the game, your items will usually be providing so much value compared to your runes that the bonuses from runes will become almost negligible. Therefore, runes help with getting an early start on building said items.

All of that said, the runes you will want to build will mostly depend on the character. For example, Jax will greatly benefit from dodge runes (since counter-attack procs whenever he dodges). Dodge is actually a very good run choice in general, as well, since there are very few items in the game that grant dodge chance. Also, champions such as Amumu would benefit from magic penetration, since he does almost exclusively magic damage, but he's also a tank, so I usually build him with flat health Marks (since he wouldn't benefit much at all from any physical attack runes), flat health Seals (until I finish buying my dodge seals - remember seals are for defense), magic pen glyphs, and flat health quintessences (which are also good in general since more health means more survivability - especially early game).

GL HF.