2.49b is very stable, and is well documented. If you are looking to complete a project in the next year then it is a good choice.
Of course, 2.5 /2.6 will eventually become the standard. It makes sense to familiarize yourself with it but some things are subject to change. There are also some improvements in regards to the game engine, for instance - http://www.youtube.com/watch?v=kTdRQwbaf4I