I flew as a courier a few times for Jupiter Air SFO-NRT-MNL, the last time 5 years ago. They use JAL for all their flights and you cannot upgrade and you don't earn miles. Back then, it was a good way to go to Asia for $300-$400, last time I checked a couple of years ago for my cousin, it was $600+.
Try this link:
http://www.jupiterair.com/index.html
I did one other courier trip for a company called Johnny Air and flew on Asiana and did earn miles for the trip. Cost was $250 back in '01 or '02. Would I do it again? No.
With Jupiter, you are known to the airline as the Jupiter courier and all you ever touch is a manifest that you hand over in Narita. Everything is above board and professional.
With Johnny Air, you are just some guy who's given up his baggage allowance to carry god knows what to Manila. I'll pass from now on, thanks.
The only reason I stopped doing the courier thing was to be able to earn miles and thus upgrades on JAL. Interesting experience, to be sure.