Alrighty, I think I've figured it out on my phone at least... maybe.
I just took a 860 mile trip fron NY to KY the week before last, then back again on Saturday. On the ay there, from the beginning, my phone started with 80%. I was navigating and streaming pandora. While doing this, my phone actually charged to 100% and stayed there for the whole trip. I was running the vanilla FRF57 ROM with P3s 1.25 GHz (that was actually a 1.1 GHz - labled wrong) kernel.
On the way back, a few things had changed besides the car and charger. My phone started the trip with 90% and eventually discharged to 30%. It actually randomly rebooted once in the first 90 mins of the trip. But I think it overheated. After I got back to the home screen, SetCpu widget said my battery was at like 125F (can't remember C., do the conversion). I was also running an extra app on top of navigation and Pandora called Instamapper that would send my GPS coordinates out every 5 secs so my wife/mom could track my location in real time. I was also running NexBeast v0.1.1 (FRF57 based) and Chevys 1.1 GHz LV kernel.
So all that changed was my ROM, kernel (that should have been using less power on the way back) and I was running an extra app that sent out my location every 5 secs. Oh, and I got rid of my Engadget widget on the way back to lessen network usage (was using the most according to spare parts while I was visiting there).
Luckily, 5 hours into the trip, I started calling people to keep me company (and alert, ironic, eh? Hah, it was via BT in-car hands free though

). During my 2 hours of talking, my phone charged from 30% to 100% since it wasn't using 3G constantly for Pandora and Instamapper (navigation still worked perfectly while talking though, cached map data FTW

). Then it stayed at 100% for the rest of the trip.
So, with all that, I think I can conclude that TEMPERATURE was the big factor that decides how well you battery charges/discharges while in use. I say this mostly because after my phone calls on the way back, my battery stayed charged while using it exactly the same way as I did when I started the trip (using navigation, Pandora and Instamapper) and NOTHING had changed besides temperature in the ccar. When I started back, it was like 95F out and I had the AC on in the car, but the vent wasn't pointed at it and it was in direct sunlight at that time (when it rebooted too). After the random reboot, I pointed a vent at it and it was good the rest of the trip (still discharged until night time when I made the phone calls though).
Car is a 2005 Nissan Altima 3.5 SE (not really relevant, I don't think, but can't hurt to say) and charger is a Motorola Charger (the one with a clear plastic circle with the Moto logo on it that glows blue). I would link to it, but I'm typing this on my Droid (lol, yes, typed this short story on my phone

) and don't feel like looking it up and hyperlinking it

. Last I checked, it was on Amazon for just a few dollars.
Someone chime in on this and let me know if you agree with me or if I'm missing a variable or something about it.