My rough overview:
Early Zappa: Freak Out, Absolutely Free, We’re Only In It For The Money, Uncle Meat, Lumpy Gravy. This is young Zappa faced with the opportunity to get his stuff out and on these albums he tries to do everything he ever wanted to do all at once. There is a kind of primitiveness about these albums, partly due to crude production and partly due to the lack of virtuosity of his band members at this time. Nevertheless they do have their charm and some favor this early stuff over the rest.
Jazz fusion Zappa: Hot Rats, Waka Jawaka, Grand Wazoo, parts of Burnt Weeny Sandwich and parts of Weasels Ripped My Flesh. This is where Zappa starts to get musicians who can actually execute his ideas and a decent studio and multitrack recording to bring his work to fruition. Hot Rats is the pivotal album where he simultaneously shows his prowess as a composer, arranger and guitar hero, with jazz and classical overtones throughout. Waka and Wazoo continue this. Burnt and Weasels are transitional albums that have one foot in the early Zappa style and another in the more sophisticated Hot Rats vein.
70s rock star Zappa: Fillmore East 1971, Overnite Sensation, Apostrophe, One Size Fits All, Roxy and Elsewhere, Sheik Yerbouti. His music becomes more 70s stadium rock on these albums. His lyrics tend (in varying degrees) towards topics of (deviant) sex and groupies and silly goofy offbeat topics. There are still many showcases of brilliant compositional and arrangement genius. As the decade goes on, his choice of musicians leans more towards technical virtuosi.
80s rock star Zappa: Joe’s Garage, You Are What You Is, Ship Arriving Too Late, Them Or Us. His lyrics go over the top, trying hard for laughs and obsessed with deviant sex and occasional jibes at mass culture or politics. This is where Steve Vai is in Zappa’s circle and likewise the other musicians are of a very high calibre.
Zappa, the serious composer: Jazz From Hell, Perfect Stranger, Civilization Phase III, Yellow Shark. Self-explanatory…Zappa makes music meant to rub shoulders with Edgar Varese and Stravinsky. Some of it is created by programming a digital sampler called the Synclavier, the first device that had the technical capacity to accurately execute his compositional ideas without the need of other musicians. Some dislike the antiseptic sound of the Synclavier. Yellow Shark features his compositions as performed by the Ensemble Modern. The Perfect Stranger is a collaboration with conductor (and composer) Pierre Boulez and Ensemble InterContemporain.
The categories above are rough guides…there are plenty of albums that straddle multiple tendencies throughout his career. Also I obviously didn’t list every album. It might be worthwhile to sample albums in many different eras and see what sticks.