Runes (like the summoner) are a consistent aspect of League of Legends, they provide passive bonuses to your Champion and must be earned by playing the game.  As you level your summoner up, you will be able to add more runes into your rune book, making your champion more powerful.

As of a recent patch... you can purchase more runebooks to add to your repertoire.
For greater flexibility, you are given three rune books to place your runes, and you are able to choose which book you will bring with you to battle.  Be sure to choose your rune page to synergize with the Champion you are playing.  A popular way to set up your rune books is to make one book for each 'type' of Champion (ex. tank).  You could make one book for DPS Champions, one book for tanks, and another book for casters.

Go here for an in depth How to on Runes.