I'm a fairly recent Zappa convert. Definitely far prefer his early stuff, Freak Out, We're Only in it for the Money, Hot Rats especially. I like some of his later stuff (Inca Roads for instance) but I'm still not a fan of the late 70s/early 80s, more satirical stuff, especially in terms of production (tried to get into Joe's Garage and Sheik Yerbouti (spelling?) but didn't really enjoy them - I quite like a few tracks off You Are What You Is though).
Now I've listened to a fair bit of his back catalogue I can hear his melodic influence in more and more modern music, particularly video game music. He really had a wonderful sense of melody