For cleans, Peavey made a couple of good ones. My Peavey MX is probably the cleanest amp I've ever played, and it's a head, in a factory road case, 30 or 130 watts. Solid state preamp into tube power amp. Have fun finding one...they also made a combo version, 60 watts. You can hear my 130 watter on my player, the song "While We Cry" was done with that amp and a Peavey Patriot guitar, no effects but reverb and slight echo.
Then there's the Classic. Not the modern one, but a 70's combo, 50 watts into a 2x12. 4 inputs, so it can be run series or parallel, really good clean sound but I'[m not sure if they ever made a head. Here's one on youtube, I didn't watch, just checked to be sure it's the same amp. Mine's in need of repair now but I used it onstage for a couple of years, did a great job.
If you want to use a Fender, it can be done, just get the highest wattage you can find and keep the volume down around 3 or 4, that's how Eric Johnson gets his clean sound. A pair of Twin Reverbs, volume very low. His lead sound is a pair of Marshalls. A really high powered Fender at low volume will get a great clean sound. I can get some awesome cleans with my Super Reverb, but not at stage volume, it's only 45 watts. It starts to break up if I set the volume above about 5 or 6. But at 3 to 4 it's nice and clean, sounds great.
Watch out for the silverface Fenders, changes CBS made were not well liked by most guitar players. Mine had really boomy out of control bass, I had to swap out the capacitor that filters bass to tame it down. Stock, bass at 2 1/2 was boomy and too much, now with a simple cap swap I run it around 6 and it's excellent. I made a couple of minor modifications, that and also removed the caps in top of the power tubes that took the highs out, the really high frequencies that give it that chime Fenders are famous for. That's all I did, I couldn't really "blackface" mine, that would require a transformer replacement and a lot of work and expense, just the couple of things I did made it a great sounding amp. The only recording I have of it right now is on Southern Cross, mostly clean. I'll have more later, I'm working with these guys now but for now we're concentrating on getting ready to gig, no recording going on at the moment.
http://www.youtube.com/watch?v=iKnqSKQCIs4
Look up Pat Matheny on youtube, you might be able to see wahty amp he uses. I looked up Alan Holdsworth, the few I looked at he was running through a Hughes and Kettner. Oh what the hell you need to hear this guy anyway...
http://www.youtube.com/watch?v=zMi2mCe7CKg
http://www.youtube.com/watch?v=dIdhhAjMTLw
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