The albums that Frank was making in the late 60's and early 70's are fairly unique. Here is the best FZ discography (and more) site that I know of:
http://globalia.net/donlope/fz/lyrics/
You can see that there are a LOT of records, and they cover an enormous amount of musical ground.
I'd suggest that Hot Rats, Chunga's Revenge, Fillmore East, Overnite Sensation, Apostrophe, Roxy, and One Size Fits All make a fairly contiguous series of albums. Add in YCDTOSA 2 (an immortal Zappa release. That band was at the peak of their skills when this show was taped) for the aforementioned Helsinki concert, and you have a lot of listening to do.
The Wakka Jawakka and Grand Wazoo albums are awesome, but they are his "big band" album and don't share a lot with the rock band sound. Even given that, they do make a nice fit with Hot rats and Chunga's Revenge!
I'm not a big fan of his work in the 80's. It is a reminder to me that NOBODY escaped bad hair and questionable fashion statements

But there is some amazing music there as well. I prefer the selections that made it onto the You Can't Do That On Stage Anymore series to the album tracks. Also, live albums like Tinseltown Rebellion contain some fine stuff.
Last, the Lather (pr. leather) box set is the collection of material that is also on Zappa in New York, Orchestral Favorites, Sleep Dirt, and Studio Tan. This series has some of my favorite FZ material ever. It ranges *very* widely, so you probably won't like everything, but some of it is simply amazing. The 3cd box release is excellent.
And then you hit the material derived from the 1988 tour: Best band You Never Heard in Your Life, Make a Jazz Noise Here, and Broadway The Hard Way. In some ways this has more in common with the early 70's material. My preference is my playlist made from my favorite tracks from all three of those.
Enjoy!