A4 vs A5 SoC
Qualcomm radio baseband chip (also has the GPS built into this)
certification with national certs (FCC, in the US)
certification with carriers (Verizon, AT&T, Sprint)
Cheaper TN vs IPS screen panel (also higher power draw of IPS setup, due to inherently greater opacity of IPS)
larger battery
more RAM, base storage
^^All exact reasons why the iPhone is more expensive than the iPod touch, beyond less clear ones, such as marketing.
Also, I'd venture the iPhone soaks up most of the development costs, while the iPod touch mostly benefits from the R%D already sunk into the iPhone.