Welcome and good post! I see you've been thinking about this just a little, huh?
I think as cool as this would be, ultimately you'd be happier with a touchscreen as the main interface. I've thought about doing something similar as I have an iPaq pda with bluetooth and wifi and before I put in a regular computer I was using my pda in my car on the dash for navigation and mp3 playing (from a 1GB cf card). I have played around with some software to control my laptop over bluetooth/wifi using my pocketpc, haven't tried Netremote yet but I have used Salling Clicker (http://www.salling.com/Clicker/windows/) and it works fairly well over bluetooth and has a few plugins to control different media players and can act as a "mouse pad" for windows so you could use gestures for some front ends.
I just think the big limiting factor, like you said, is stability and if something goes wrong on the pc. While I was setting my pc up I would bring it inside and remote desktop into it but there were still times when I had to restart it if it locked up and had to hook up a keyboard to it so I could hit the occasional Enter during a prompt at bootup or send a ctr-alt-del to it. If you pc is pretty stable now maybe you could get by with just having a keyboard hooked up to it so you can hit Enter or something if there's an error during boot. I just don't just mine to be that stable and I would probably get annoyed pretty quickly if all of sudden the pocketpc wasn't working, then had to do some troubleshooting and reconnect the pocketpc and then figure that something like locked on the computer, and then drag out a keyboard or something while in the car. Plus, at least on my pocket pc (and to a lesser degree on the computer) bluetooth is just not that stable yet. Salling Clicker worked pretty well but not for everyday type use. I think there are some bugs in some of these early pocketpc's bluetooth stacks where they would kind of "time out" and I would have to do a soft reset before I could connect again.
From looking at the site Netremote may be workable since it works with Girder. Also it says on the site it can use pronto style .CCF files, which if you aren't familiar with them are the configuration layouts for those Pronto (pda sized) touchscreen remotes for home theaters. Usually IR based and the software lets you create your own custom screens and then you just assign your IR codes from the original remote and you have a custom IR remote. Used to program those a home theater company so if you had Girder setup and you could map a bunch of keys/commands it wouldn't be that hard to create a custom layout with image/buttons to send codes to Girder to then do whatever it could do on windows. (If you end up getting that far with it let me know or I can send ya some more info on that program). A little more involved but may let you make it work the way you want and make it a little more "integrated"
Ya know, a totally different way you may want to approach this is instead of just using the pda to control the pc (except for GPS), maybe look into using the pc mainly to share the media files, and then set up the hard drive/folders, etc... to be mapped drives on the pocket pc. Right before I set up my carputer I was trying to figure out a way use my pocketpc to play the media files off my laptop so all I had to do some turn my laptop on in the car and just use it as a "media server" but use the pocketpc player's interface. Turned out to be pretty tricky and I finally had gotten it to map a drive when connected through a wifi or bluetooth network but I again ran into issues with bluetooth and for me to use wifi I have to put in a cf wifi card so I didn't want to use that all the time and not use my cf 1gb card. But that could be another route, use the pocketpc's applications (GPS software, media player, etc..) but then just get those to access a mapped drive off the computer. Of course you'd need to hook the pocketpc to the audio, etc... and may lose a little of "portability" you had mentioned.
This is getting kind of long but those are my 2 cents, I thinks it really neat to use my pocketpc for stuff like this and have played around a good bit with a few different media control software setups but seemed like it was only good for occasionaly usage when I had time to tinker with it (and not driving in the car). And at least on my pocketpc it handles network connections really weird and took me even a while to get it to work over a bluetooth network, had to finally give it a manual IP and play with several network settings, plus everytime I wanted to play with it I was going though several menus to connect, then to bring up the right software, etc... which I didn't want to do in the car. So if you do go this route keep it fairly simple and straightforward by maybe just using the pocketpc to control winamp or another media player using netremote and also for GPS navi, and not to worry about full control of the computer. If you go the full control route it will take some tweaking but I'd be interested in what all you used.