I looked at bunk beds extensively about a year ago and asked for lots of recommendations. I would stay away from the inexpensive beds at kmart and ikea. I think all sets can be separated into two beds.
I looked for weeks on Craigslist, just in case, and eventually a beautiful, practically unused set came up - it was from a good furniture store and had all the paperwork, etc. Friends of ours used an online furniture store and were happy - I have a bunch of stuff I bookmarked, but I think the site might have been csnbunkbeds.com.
Also, check the consumer products safety commission recommendations. They might make recommendations, but from what I can tell, manufacturers don't necessarily have to follow them. http://www.cpsc.gov/businfo/regsumbunkbed.pdf
Oh, I also meant to mention that our bunk beds are simple. They are so heavy and the room is small - we didn't want to add any more weight to the furniture than we had to by adding storage shelves or whatever.