There have been many threads covering this topic already, so I will keep it brief, naming mostly the pro's of each:
Melamine - Only one "window", so the animal tends to feel more secure, as opposed to living in a "fishbowl". Wood tends to be a better insulator of heat than glass.
Glass - Can look really good. Not affected by humid/damp conditions (melamine of course can be sealed, though not as effective as glass). Can also house water "out of the box".