Dang, where to start?
Bottom brackets. Not only has the market moved from square taper to Octalink, but it's also moved beyond that to external bearing cranks. You are two generations behind my man. If I was you, though, I would stick with what you have. You can still get decent Shimano units, like a BB-UN54 level. This is gonna be about $20 new, nothing major. If you switch, just go to Octalink II (external bearings). I have XT Octalink II cranks on my Blur, no complaints, LX Octalink II on the geared HT (race bike sorta) and FSA outboard bearing cranks on the 'cross bike. Both have been solid, although I did have an arm on the 'cross bike come off last season in the middle of a race. The bolts must have loosened or something. The advantage to outboard bearings is significantly bigger bearings, which does lead to longer life.
Shocks. Your Judy is more like a 80mm fork, so about 2.5". I run Fox stuff, love it. Advantage in my mind, simple, well made in the USA, excellent parts availability. The premier MTB fork tuning house is right here in Colorado, PUSH. They're up in Loveland, they have every single part for Fox shocks and can turn around repairs and rebuilds in a day or two. But I've also rebuilt Fox forks, it's not tough to do yourself. But nothing wrong with Zokes or Manitou IMO. Rock Shock has gotten a lot better under SRAM ownership the past few years, for a while in the late 1990s they were utter crap. You can still get 80~100mm forks with canti posts, that's not a big issue. Also you can run a disc in front, cantis in back, that's not a problem.
PUSH Industries: http://www.pushindustries.com/
Brakes. I LOVE DISC BRAKES! If I had to only keep one advancement in the last 15 years it would be disc brakes. Hand's down, hardtail, rigid fork, single speed, 26" wheels, just as long as it has disc brakes... In Colorado they are the bee's knees. Seriously.
I have a Santa Cruz Blur LT. It's not a super boutique bike, but it's not all that common. I see a lot more Specialized, Yetis and Treks, but fewer Moots and Intense. About the same as Ellsworth on the trail. I ride a large, you are welcome to give it whirl sometime. I run a 140mm Fox Vanilla and it's mostly a mix of XT and SRAM X.9 level stuff. Pretty utilitarian. If I was gonna buy a bike right now, it would be most likely a 3" dual squish 29'er of some sort or maybe a HT, although I'm really looking forward to the 650C bikes to get established. That's a 27.5" tire and I think a better balance for a ~4" trail bike.