To me they are all good guitars, thats why I have all three.
What I use em' for...
Jazzmaster - Killer neck pickup, lots of tonal variety with the master volume (it's like an SG and a Telecaster in one guitar). However, when I built mine, I did make some changes, like I preferred a hotter bridge pickup than usual (8.8 Kilo-ohm), and wanted 22 Frets instead of 21 for a little help in the bending up to E or higher category.
Jaguar - The Jaguar is probably the only guitar I would feel comfortable buying off the rack just before a gig and playing it right after in a live situation. The Jaguar always sounded a bit like a P-90 Les Paul to me, since with the volume in the right position (on mine it's full up because I still have those 500K pots in there, but my Jazzmaster and a classic player Jaguar is inspiring me to go the stock 1 meg route before too long). Despite the oddball switching for the pickups (which I'm quite used to, I've figured out ways to quickly snap my fingers over the switches to change to whatever combo I want). Also, it seems to me, like the Jag-Stang, all the curves and countours are in exactly the right place, same with the Jazzmaster, those three I can sit around and play for hours and never feel tired.
Mustang - I really find the Mustang brings out a very weird use of pickup selection that I never thought about. At first I picked it up to replace the Explorer copy I built as the "out of phase" guitar as the Explorer had EMG pickups installed and could no longer do the whole "out of phase" sound anymore. I typically spend most of my time on most guitars playing bridge pickup only with the knobs wide open at 10+, but with the Mustang I'm finding the Out of Phase sound is PERFECT for crunchy rhythms with high gain, and has a really nifty music box quality to it when clean. Also, my Stang has been an experiment in using a ONE SPRING Dynamic vibrato for awhile (I took the other out because the bass-side post is seized), the stuff I can do on one spring surprises a lot of the locking trem users I've met. People say a Kahler's smooth, but to me, the Dynamic Vibrato with one spring beats em' in smoothness.
However, my Jag-Stang remains the #1 in my collection for several reasons. The first is the sentimentality, that was the first Fender, second offset, and probably the best guitar I've ever had. Much of my sentiment is similar to SRV's towards his 59'/63' "#1" Strat. In 10 years that guitar has only gone down ONCE, the only one that beats it is the Jaguar I've had half as long. Then there's the switching scheme I've perfected and gotten so used to it's 2nd nature, and that guitar has the 2 spring Dynamic vibrato that acts like a quasi-trans-trem. Despite the mods, the base instrument was amazing from the get go, I can STILL, despite having GROOVES in my frets, crank the action all the way to the fretboard and still play chords with minimal to no buzzing, and that amazes me because by appearance it seems I need a fret job, but nope, sill plays like the first day. Plus that neck is my favorite neck profile, if I ever had the money, I'd get some copies made for future Jags and Stangs. Since the tuner replacement the only achilles heel that guitar has ever had is gone, I've not had to tune it but once or twice in the last month.