In no particular order
Green Ronin
Troll Lord
Bastion
Fiery Dragon
Malhavoc
WotC
AEG
Atlas
Bad Axe
FFG
That being said, however, I don't know that I mind too much if Atlas drops off the d20 market. They have an excellent stable of games that should compete for my dollar with non-d20 systems.
I have no problem with a company choosing to focus on things like Feng Shui and Unknown Armies when those serve to complement my d20 playing so well.
That said, the reverse is also true, while I understand their motivations given the status of Oriental Adventures from WotC, I can't say that I'm happy that AEG is abandoning their d20 support for Rokugan.
That setting worked very well with d20 and even, I would argue, better with d20 than it did with their own roll and keep.
Furthermore, I would say that this list is really pretty arbitrary, I mean, I could list the publications that I use most, but I am happiest with d20 when I am able to find publications to fit my specific interests and whims so I range pretty widely in my purchases, am happy with the products I get, and sad when a company goes down that could have made the product I needed to fit the mood that month.