In my (VERY) limited experience with mods, I've very much preferred OBMM. I find it a lot easier to use, and it reads .BSAs just fine. Can't really complain. I've embarked on the surprisingly difficult project of an FCOM installation, along with dozens of other mods, many of which require me to use Wrye Bash and BAIN. I've had a lot of trouble with this and my copy of Oblivion has been out of order for about 6 months now. (Although that's mostly due to my procrastination.)
Anyways, OBMM is quite a bit easier to learn in my experience, but supposedly BAIN has more features and is more efficient once you know what you're doing. That said, more mods support OBMM installations.
Can't really give you a list of mods, but I'm following http://www.gamesas.com/index.php?/topic/1119325-50steps-to-stable-fcom/page__p__16452602entry16452602 at the moment. Good luck installing it all within an hour, though.