I like Santa Sangre...Ebert's recent article describes it pretty accurately, so if it sounds like something that would interest you, you should definitely check it out.
El Topo isn't as good. It's got some really kickass stuff in it, but there's also a lot of symbolism that's just...well, too obvious for my tastes. But it's intensely memorable. If you're into cult classics, it's worth owning. If you just want to see it, most major cities will have a cult or underground video store with a copy for rent. It's not too hard to get ahold of.
Supposedly, the film he's getting to work on now is The Son Of El Topo. And Marilyn Manson is very much involved.