A quick list off the top of my head.
Transit
Let the Happiness In
Wave
Darkest Dreaming
Under Ingrid's Wheels
Earthbound
Pop Song
A Fire In The Forest
Blackwater
The First Day
…and the two conclusions I draw from my favourites are that a) I don't think Syvian / Fripp made anything like the best of their material when compiling The First Day and b) He should do a whole album (solely) with Fennesz.