I've seen a few threads over the years regarding favorite tones, but rarely are the clean tones mentioned.
Eric Johnson on Ah Via Musicom and Venus Isle....pretty much his clean tone in any era is perfect, but I really love the clean tones on those two albums.
Petrucci on I&W and Falling Into Infinity. On I&W, man, I think that clean tone pretty much became the benchmark for all my clean tones, chorus, delay and compressed all to fuck, ultra scooped. The ending of "Learning To Live"....really, all the cleans in that song. (Never understood why he never played the intro to "Pull Me Under" live without a ton of delay on it....he's always played that live with just a shitton of chorus)
Hendrix - even though it's not TOTALLY clean, stuff like "Wind Cries Mary" and "Little Wing"....I just love that round, tubey Strat tone.
Eric Johnson's tone as you mentioned is definitely up there and was the first guy I thought of actually.
However, I am also a huge fan of DeGarmo's & Wilton's clean tones in Queensryche (Operation & Empire).
Steve Vai's tone in "Tender Surrender" is to die for.
+ 1 on Perrucci's I&W.