It has its own JVM (currently, I think it's at version 1.3). For agents that run on the server, you should be good to go. For agents that run on the user's machine, you might have to make sure that notes.jar is in the classpath, though I'm not certain about this...
Also, be sure to check out the R6 forum on notes.net.
I use IBM's notes.net forums on occasion, but I've never had good luck there -- kind of like Sun's Java boards. I wish there was a "NotesRanch"!
I wrote a Java agent that we're going to be able to test in production. (Without going into the gory details, this is a Dilbert-ish corporate environment in which Groupware's production standards are very unclear, and we get charged ridiculous intra-company fees for anything we try. But I'm sneaking this agent in with an unrelated design change, so we'll be able to verify that it actually works in production.)