Hazel:
For starters, spools are cheap compared to a locker and I really prefer them to an automatic locker in a short-wheelbase rig. If possible, I'll save a couple hundred and go with a spool in the rear of a mostly-trail rig. For a street-driven, short-wheelbase rig it's totally worth it to me to pop the extra for a good selectable locker like an ARB or Ox. The convenience of having that open diff on the street is nearly priceless.
As for swapping in larger axles or upgrading the stock ones, tire size is usually the determining factor for me. If I'm going for a vintage-vibed early CJ with 31s, I'll be more than willing to leave the stock axles in place and throw money into other areas of the vehicle, like a replacement frame. However, if I'm looking to run 35s, 37s, or larger wheels with bigger tires, I'll look into upgrading to a Dana 44, Dana 60, or Ford 9-inch, depending on budget. It really is cheaper sometimes to just pop the dollars for the replacement axle assembly in the first place rather than make piecemeal upgrades with stock assemblies. Very few Jeeps left the factory with axles capable of running 35-inch or larger tires.
Trasborg:
This is one place where I've never been very good at leaving well enough alone. I don't think Jeep should have ever put any less than a Dana 44 axle assembly in any vehicle. Even if I have no plans for bigger tires, as soon as the stock axle starts showing signs of weakness, even if it is something as simple as an axle seal leak, I'm in the junkyards or online classifieds looking for that Dana 44 (at least). Another axle assembly of note is the Ford 9-inch. With my proclivity for leaving the Jeep relatively low and the availability of decent gearing options, the low pinion of the 9-inch doesn't bother me much and the ability to build it up as needed is great. However, all factory Ford 9-inch axles need a truss for any real off-road abuse.
Comfort, Convenience, Safety
Cappa:
Most mid-'90s-and-up Jeeps are pretty comfortable and safe for all but the most abusive trails. Bad seats in an old rough-riding Jeep can make a wheeling trip a bummer, though. Aftermarket suspension seats are always a welcome addition in my Jeeps. But I gotta admit it's one of the last things I attend to. My comfort comes secondary to solid mechanicals. But it really depends on how and where you go off-road. If you're going where abusive rollovers are handed out like candy on Halloween, you best spend some coin on a solid frame-mounted cage, seats, and harnesses. And if you're building a trail rig and spending money on a stereo before you buy a locker and winch, you deserve to be stuck alone in the woods overnight.