My favorites in order probably would be
1. Dragon of Doom
2. Mountain of Mirrors
3. Pillars of Pentagarn
The first 6 by Rose Estes were the best with the exception of Book 13 (Dragon of Doom).
I have (and still have) up to book 34 (Claw of the Dragon).
They had other Endless Quests books published later (I don't have most of those) which included
[Dungeon of Fear, Castle of Undead, Secret of the Djinn, Siege of the Tower, A Wild Ride, Forest of Darkness, Night of the Tiger]
The best Endless quest wasn't really Endless Quest. They started as Super Endless Quest books (I got the original because it was a Dragonlance Book, and I LOVED Dragonlance at the time) but then evolved into AD&D gamebooks.
There were 18 of them, I managed to get (And still have) that entire series. Selecting the best ones of those would be harder.
Then there are the new ones (6 thus far, or at least I have 6 of them). I'd put them more on par with Spell of the Winter Wizard (which is NOT one of my favorite Endless Quest books).