The thing to remember is that most of those emulators are going for "tube" clean. In many tube amps there is some harmonic coloration due to the nature of the tubes themselves. A tube distorts gradually and when measured there can be a lot of harmonic distortion in the signal, even though there is no audible distortion. The human ear perceives it as "warm" but not distorted. There may also be some light tube compression going on as well. This is the difference in a Roland JC-120 clean sound, which is icy clean with very little distortion and a Blackface Twin/Pro Reverb which may sound clean, but there is some harmonic coloration even in a signal that sounds clean.
I personally have come to like the Voxy clean tones. Chimey and warm, but nasty and vicious when pushed into distortion. I've owned a few nice Fenders, but I always ended up getting rid of them as their clean tones just don't do it for me.
Mesa amps started as modified Fender amps. So they have roots in the Fender clean sound.
The output tubes themselves affect the clean tone as well. Tubes like the 6L6 and 6550 are inherently clean until pushed too hard. Tubes like the EL84 and EL34 are more dirty sounding.
Originally Posted by Eric