I for one prefer the EEPROM's as they do not require anything special to program. They also do not need a special UV light to erase and can be re-written a byte at a time if you want to.
When I built SBC-1 (a long time ago), a created a home-made programmer that used the 8 bit data lines of a PC parallel port, feeding 74373 latches to hold the address and data values while driving the /WR pin from a status pin. I use QuickBASIC in DOS 6 to drive the port and program the EEPROM.
I later built an EEPROM programmer driven from a 6522 VIA and programmed using 65c02 code. it can be found here: http://sbc.rictor.org/28256.html
About 10 years ago, I bought a serial port driven programmer from EBAY for about $50. It has served me well for programming 32kx8 EEPROM's for all of the SBC-2 & SBC-3 boards that I have created.
Feel from to ask me any questions about doing any of this yourself.
Good luck with your project.
Daryl