The best in my opinion are Beyond the Wall, which accurately captures the flavour, setting and mechanics of authors like Le Guin, The Black Cauldron, Robin McKinely and John Bellairs. It is also the best example I've seen of how to have a truly low magic setting that still feels mythic and fairy tale-like. It has excellent suggestions for how to present the underworld, goblins and fae, etc.
The other, only available in hardcopy from Lulu, is The White Hack which is such a radical rewrite of D&D I think it can be considered its own system, although with a D&D chassis. I think it is very well done, with much more flexible approach to class than D&D for instance, although I suspect it would be too Scandinavian for many, especially with its nearly freeform magic system.
The Black Hack is pretty much just a system, but stripped down and different enough from core D&D to lift it out of being a retroclone I think. Lots of cool little ideas one could take and use without using the whole system, although my limited experience with it found it plays very well at the table. The best of the D&D plus house rules systems I think.
In many ways these are all different enough from D&D that I wouldn't really call them retroclones as they are all about taking D&D and doing something different with it, not recreating some imagined play style from the past.