I've told this story before, but can tell it again. When I bought my Mesa I actually was planning to buy the F30. However, the salesman said to try them both and then make my decision...adding that many ended up with the F50 after trying them side by side. I had a friend along with me who's got a great ear and we ran both through their paces side by side. Our conclusion was that the F50 had more clean headroom on the clean channel and that the gain on the lead channel on the F50 did NOT get as buzzy at the higher gain settings, nor did the F50 compress as quickly as the F30 (i.e., the F30 got squishy at lower gain settings than the F50). Mind you, the differences weren't huge, but they were noticeable to both of us. So I felt the F50 better suited my tastes on both channels. Volume wise, very little difference. Lastly, I prefer the Custom 90 speaker in the F50 to the Vintage 30 in the F30. The C90 has more bottom end and is less boxy sounding (which comes from the V30s accentuated midrange response). So in the end, I decided the for me it was worth the little bit extra the F50 cost.
Edit: Tone wise, they were very similar. My guess is that the difference made by the power amps isn't all that noticeable until you've really got the amp cranking...and both of these amps are so loud I don't usually crank them that much. I've got a Weber attenuator now, but I don't find that the amp sounds that much better with the power section really pushed hard, so I rarely use it like that. Mesas get most of their gain and tone shaping from the preamp (cascading gain and all). The power amp is kind of the salt...most of the flavor comes from the preamp, so that's probably why the two sound so similar despite the different power amps. Again, I expect the difference might be more noticeable at high volumes....but you'd better get some earplugs before you do that...and if you're mic'ing your amp at gigs, chances are you won't be pushing your amp hard enough for the power section to make a difference anyway...I never did when I gigged like that.