This topic contains outdated information
I want to give you some information about creating custom texturepacks for the game, since this feature already exists, but it is not very obvious how to use it. Please note that you cannot customize your GUI this way, it is planned but not implemented yet.
Alternatively you can also have a look at the tutorial by @Nova, where he describes how to replace the original textures (also works for the GUI): How to make custom textures into the game - Warning: No official way for texture packs it's just for the purpose of testing
First of all, create a new folder "Texturepacks" in your game directory. Inside this folder, you create a new .zip file which should have the desired name for your texturepack (e.g. "myTexturepack.zip").
Now you can add the textures you want to replace. This is going to be a little bit complicated, since the replaced textures must have the same name, format and dimension than the original ones (find out more about this in the linked thread above).
For example, create a folder "World" in your zip, containing a "stone.jpg" texture to replace the stone texture (which you see mostly in caves).
Finally you need to specify the "custom_texturepack" key in your config.properties (in this case: "custom_texturepack=myTexturepack.zip").
That's it! When starting the game, you should be able to see your new textures
Please note that we will replace most textures by .dds textures in the future. This requires you to also use dds textures for your texturepacks (and also when replacing original textures).