I'm a big Zappa fan, especially of his earlier work, and think his albums were generally well-recorded for their time and style. The Grand Wazoo is a good recording, with largely jazzy music. Uncle Meat is a favorite of mine, with a wide range of styles, crazy editing, and good recording quality. I have original pressings of these on Zappa's Bizarre label. Mothermania is a nice anthology of his first few albums which Zappa himself assembled, and contains much of the best music from those albums. I like the Flo and Eddie period, in which he hired two singers from the Turtles and some more competent musicians such as George Duke. The 200 Motels soundtrack album is one of my favorite all-time albums, with a phenomenal variety of musical styles, although the recording EQ leaves something to be desired. If your system is bright, this recording may have some painful moments.
Starting with Overnite Sensation Zappa's albums took a more commercial turn and were more successful commercially. He relied on simpler rock and R&B music and humorous lyrics that he often delivered himself. But he also released albums of his more serious music in the contemporary classical genre, with orchestras such as the London Symphony Orchestra. He complained about how poorly orchestras played his music, which was often very challenging rhythmically.