UPDATED for 1.8!
Currently there are six kinds of wood in Minecraft. Oak, Spruce, Birch, Jungle, Acacia, and Dark Oak.
Acacia and Dark Oak are more recent additions to the Minecraft family, and while Dark Oak is similar to Spruce, Acacia quickly became popular for it’s red hue, which can be turned in to stairs and slabs for red roofed housing creation!
Each type of wood is slightly different, and all look a little bland on a default texture pack, but when used correctly, you can create beautiful structures using these wooden planks and logs in Minecraft.
My favorite mix is using the contrast of darker Spruce or Dark Oak logs with Birch (Light) planks. Using the dark wood to outline a building and filling in the walls with either Oak or Spruce looks great.
The only wood I do not really use too often is Jungle. Infact the only real time I have used this wood in construction is when I wanted to use Cocoa plants to create a Chinese lantern style effect (These guys grow on Jungle wood).
Deciding which of these types to use very much comes down to your own design preferences, My advice is try them out and see which ones you think work well together.