Personally, I like Fallout 3 Archive Utility, it runs on Skyrim without errors and without requiring setting up any Fallout files, like I believe FOMM does.
It does require Java to run though, but that's not a huge issue...
http://www.fallout3nexus.com/downloads/file.php?id=34
(This question comes up lots. Would be nice to have a "Read Me First: Important / Current Modding Info" sticky thread.)