Will flesh this out later, and to be honest it still seems a bit of a black art. But one thing I firmly believe in is independent 12V chargers for your batteries (i.e. if you have 4 batteries, either get a 4-bank charger or 4 separate ones). If you try using a 48V charger (like on golf carts) - you will eventually get an imbalanced battery pack - which eventually will cause the weak batteries very early death.
Other than that the main thing to look for is charging efficiency and marine rating. I just bought a Genius charger and it seems to give the batteries a better charge than what I've used before (I have a slightly higher starting voltage and it seems to fade more predictably).