Thank you for a good spot to jump in!
1) Apple spent a little over $2 billion this year on R&D. Even if every penny of that went to just mobile devices (not ATV, Macs, etc), that would only be $2.4 billion / (iPhone:80million + iPod:40m + iPad:40m) = $15 per device.
2) Phone related licensing fees are probably around $40 per device.
3) Subsidies are loans by the carriers to customers, not loans from Apple.
Total = extra $55 for R&D and licensing for a phone, along with about $30 more in parts, or just $85.
Even if we're generous, and make the R&D be covered totally by just the iPhone -- plus double the licensing fees -- that's still only $140 more for a phone.
So those things alone don't explain the $250 vs $700+ retail price difference. Interestingly, other companies sell PMPs and phones for about the same price difference.
PS. Estimation corrections welcome. I have a bunch of nine year olds playing around me today, and it's hard to concentrate