It petty much depends on exactly what type of wood you're talking about. Much of the wood sold for reptiles is Grapewood. Grapewood is a soft wood containing tannins which will seriously discolor your water if not boiled out. Grapewood also has a tendency to develop a nasty slime after being submerged for a while. Sometimes the slime will go away, sometimes it won't.
While Grapewood has some interesting shapes and is inexpensive, you're setting yourself up for a lot of aggravation if you try to use it in an aquarium. Believe me, I know.