Richie said: yeah, the pickups are nearly identical to strat pickups, but underwound a bit. also strats use 250k tone pots whereas a jag uses 1 meg pots. So they're massively trebly. They're only really meant to handle clean and lightly overdriven stuff, but I'll be damned if that's all I'm gonna use mine for.
Actually, that's a little off......
http://www.provide.net/~cfh/pickups.html
The Jaguar sample here has 200 more winds than the Stratocaster, also, looking at Seymour Duncan's offerings, it's 6.8K ohms, not 6.4K or less like the Strat. The more resistance a pickup has, the bassier and warmer the output. Of course, this is not true of ALL Jaguars, as most of which were made in the 1960's were scatterwound and slightly random. The one vintage Jag I have played had to have had pickups on the hotter end of the spectrum, as it really got saturated really well on a Mesa Heartbreaker combo (which was more designed for a classic rock type sound rather than the shred/metal I was doing at the time).
I have also heard some of the newer AVRI and CIJ/MIJ Jaguars, and they all sound a little different from one another. The AVRI on Webrocker's page is definatley thinner sounding and chimey compared to the vintage one he plays, I think the MIJ/CIJ guitars are the same way to my ears, though a little moreso.
Also, a reissue of anything vintage is only the same as the guitars it's clone from as far as construction, save a few overseas differences that lead to some odd difference between the Jaguar CIJ/MIJ models and the AVRI models, and the Vintage guitars they are designed to be reissues of. I've also seen this trend with Mustangs too, I listened to at least 6 different ones that were bone stock, and have played one, and all of them sound a little different.
Likewise, I use cool rails in my Jaguar because I don't see a point in changing to stock pickups (they came in that guitar), they sound pretty darned close to the Vintage Jag on the Webrocker Offset guitar site. But if I pulled them out and put them in another Jaguar, they would probably react differently because of wood density, and manufacturing differences, as well as setup, intonation and so fourth.
As far as I would have if I built another Jaguar, it would be like this...
Neck Pickup - Lollar Vintage Jaguar, slightly underwound, probably around 6.2-6.4K Ohms (to take out some of the lows to keep it from getting muddy).
Bridge Pickup - Lollar Customized Jaguar, overwound to around 6.10/7.3K Ohms, to get a little extra bass, but not too much more out of the guitar, while still keeping the overall Jaguar tonality there.