The main difference is in how much memory it has. Right off hand I don't remember the specific numbers but basicially the revision B has more (twice as much I think). The reason Roku increased the memory was because with some applications the Rev, A was a little short on memory and this caused issues. Anyway, there was a simple workaround and that was using a swapfile on a compact flash card. So basically if you get a rev. A with certain applications you may need to setup a swapfile on a compact flash card and if you get a rev. B you likely won't have to. However, it is not always necessary to use a swapfile on a rev A. I don't normal run with a swapfile on my rev A and I have no problems but I mainly only use cinemasix on my roku and stream to it from TSreader. I rarely use any other applications on the Roku. So whether the difference will even matter at all will depend on what you do. For more specifics see the forums over at the roku website. There you'll find details on how to setup a swapfile and what applications may need it.
If I'm not mistaken there is one other difference and that is that the rev. B comes with a remote that is said to be a bit more powerful and perhaps with a bit more range.