Now that I have an iPhone myself, I did a simple test which confirmed that IPv6 support is not active for the iPhone. The test was done with firmware 2.0.2.
To test it I added a web page on my Mac (using Apache 2, with IPv6 support enabled), that pointed back its numeric IPv6 address (something like
http://[[2001:4978:15d::1]]/ ) and when I clicked on the link Safari told me that the "Operation could not be completed. Address family not supported by protocol family". Additionally there are no square brackets support on the keyboard in Safari on the iPhone, preventing input of IPv6 numeric addresses.