The Atmel RZRaven AVR boards as well as the USB stick both contain 10-pin, 50-mil JTAG interfaces. The pins must be soldered on by the user but are included in the evaluation kit. An 50-mil to 100-mil adapter allows connecting the JTAG interfaces to programmers.
The Raven boards but not the Raven stick also include 6-pin, 50-mil ISP interfaces. The pins for these must be soldered on as well but no 6-pin units are shipped with the evaluation set. However, as they are only header pins, the 10-pin units that ship with the evaluation set can be broken off to create 6-pin units. (See link, search for "ISP connectors").
The ISP interfaces on the Raven boards are faulty; VCC and GND are not connected for the 1284P MCU. Atmel has suggested a workaround by jumping those pins to the VCC and GND pins for the 3290P ISP header. (See link, search for "7 July 2008"). The Raven stick does not contain an ISP interface at all, however, clever hacking can change that. See here (search for "USB stick") and here for more information.
To summarize, it is possible to use a cheap ISP programmer with the Raven boards yet the USB stick will require quite a hack. Nevertheless it is possible and has been done before.
To use JTAG to program the Raven boards and stick, the header pins included with the evaluation kit must be soldered on. JTAG programmers can be expensive. The AVR JTAGICE mkII programmer goes for around 265€. Clones are cheaper, for example the Olimex AVRISP-500, and while the clones don't allow debugging more importantly they do not support all AVR chips. The AVR Dragon goes for around 50€ and supports JTAG.
The debugging capabilities are artificially limited to the first 32kb of an application so as not to cannibalize sales of the JTAGICE mkII. The dragon also supports debugging now on all AVR chips.
The Dragon seems the best choice. It supports the most programming methods but it needs to be set up and tested before it will work. Debugging on Linux is supported. I have also checked that it supports the ATmega1284P; the AT90USB1287 and ATmega3290P are off-board targets. Note that the Dragon differs from the AVRISP programmer in that the ISP pins do not supply power to the target chip.