Yes, definitely thinking about all those Barry Guy sets on Not Two that sort of kicked this whole thing off. Those are all uniformly excellent. Fundacja Słuchaj also got in on the action and also put out a number of fantastic ones. Some specific favorites:
Various - Long Story Short (arguably the best of them all in my book)
Ken Vandermark - Resonance
Joëlle Léandre – A Woman’s Work
Zlatko Kaučič – Diversity
Steve Swell - Kanreki: Reflection & Renewal
Agustí Fernández – River Tiger Fire
The Black Saint/Soul Note boxes were a great line. I would say the Bill Dixon is completely essential, and the Threadgill, Motian, Hill, Lyons, Haden, and Ran Blake ones are also very, very strong bodies of work. The ECM Old & New Masters line was also great in this vein-- the Motian and Arild Andersen ones especially.
A few others, randomly:
Various - FMP Im Rückblick - In Retrospect
Sven-Åke Johansson – Blue For A Moment
Sven-Åke Johansson – The 80's Selected Concerts
Various - Just Not Cricket!
Jürg Frey – Weites Land, Tiefe Zeit, Räume 1 - 8
Bengt Frippe Nordström – Vinyl Box
Peter Kowald - Discography
I would also second the Hemphill on New World, Wood Flute Songs, Nation Time, Evan Parker, Ahmed, and all the ones on No Business.