Well, the Betelgeusians are still without equal as my personal favorite obscure Star Trek alien (I've blogged about them before; they have the added mystique of never having been seen clearly) but I found two races recently that I hadn't known much about before. And there isn't much to know, appaarantly.
My girlfriend bought me a set of Deep Space Nine Season 1, and I got curious when I saw a few Markalians (unnammed as such). Mercenary characters catch my eye, what can I say. As for Caitians, I had previously seen them as characters in books, but had not known they were seen breifly in the movies, but especially The Animated Series.
http://forums.startrekonline.com/showthread.php?t=176953 Also, the "Shroomies" I always imgined them to be the Tzenkethi http://drexfiles.wordpress.com/2009/06/30/bio-diversity-department-the-shroomies-with-john-teska/