Zappa's synclavier music is definitely not "throwaway", as someone above put it. Civilization Phase 3 has some of most interesting compositions, a lot of which he wouldn't have even tried with real musicians.
I really like Trance-Fusion. Most of it is from the '88 tour, which featured some of this best guitar tone; the soloing sounds great, even when at times it isn't particularly interesting. I'd say his soloing from '88 was his best since the late 70s.