Here's what I've used in my Mesa Dual Rec:
Mesa Preamp (good overall)
JJ Preamp (very hot/gainy, would be too harsh with all JJ's in my mind)
Mesa 6L6 (Smooth, bassy (almost too much)
JJ 6L6 ( Tighter, even smooth high gain distortion)
Mesa EL34 (Weak, too much mid/treble)
JJ EL34L (Perfect compromise for EL34 crunch and tight low end)
JJ EL84 (with converter, otherwise it's a different pinout)
Mesa 5U4B Rectifiers (Mushy, inarticulate in my mind)
JJ GZ34 S Rectifiers (Tight, perfect sag)
The more I toyed with the preamp, the more I realized I like the JJ in V1 and the stock Mesa preamp tubes in the other 4. I prefered the JJ EL34L tube the most with the Dual Rec but it didn't have the thunderous low end of the Mesa 6L6 and the JJ 6L6 were.. so I alternate back and forth. The GZ34 is an awesome rectifier unfortunately I had a bad one and I had to switch back to the Mesas. I plan on putting the JJ's back at some point permanently.
There are lots of options in the tube realm, research your companies a little bit and find out what each tube offers, etc. Here are some resources:
http://www.dougstubes.com/
http://www.eurotubes.com
Also doesn't hurt to search for people who are running the set up you are going for.. a lot of times there are comments that might either sway you away from a choice or interest you more, etc... keep in mind tone is very subjective so look for the middle of the road responses.