hi,

you have not indicated the vendor.

For example, Atmel:

1) There is AT89S8252 with in-application programmable built-in 2kb EEPROM.
2) There are alot of chips with built-in bootloader and user API which allow user to write in program flash from application ("on-the-fly"), namely:
(A)T89C51RB2/RC2/RD2/ED2/IC2/ID2/CC01/CC02/CC03/AC2 and even more (visit their site to see the list of them all). Some of them have built-in EEPROM as well.

Regards,
Oleg