I'm just getting into the paperless caching and I'm going far enough to try to combine all of my caching "tools" into one device. Santa dropped off a new wireless/bluetooth Pocket PC yesterday and since I had an idea of what I was getting, I have been doing some research into what I'll need.
The first is to set up pocket queries, something I've been using for a long, time now as it makes caching trips much easier.
I've used several applications for organizing/managing those .gpx files and my favorite is GSAK because it lets you do so many things with the file before you push it to the handheld.
On the handheld, I'm using GPS Sonar. Although I'm using Windows Mobile 5.0, it runs just fine.
For GPS interface/mapping, I'm doing a trial with Bee Line GPS (http://www.visualgps.net/) and I'm happy with it so far - it's got geocaching features built into it so your GPS nav data and waypoints are all integrated into one happy package. I don't have street level maps but if I need those, I can use pocket streets and export street level maps to the thing and navigate with those. I like the challenge though.
My GPS rcvr is a bluetooth unit that sits on the dash (creatively designed holder in word) while in the car and clips right onto my camelback/geostash bag when I'm out of the car. In addition to the GPS holder, I'll be getting a Pocket PC holder and then both devices can be on a charger while in the car if needed. So far, my battery life has lasted longer than I can on a winter caching day.
No more three ring binder and GPS (verion 1), no more GPS, Palm Pilot and notebook (version 2) and finally, no more GPS and Pocket PC (version 3). Now it's the pocket PC and my hydration pack and I've got all that I need. No more papers to loose and before long, GSAK will have a better macro that will allow me to push my cache notes directly to GC.com when I sync the Pocket PC!
It can be done, it just takes some time to figure out what software meets your needs.