fpga4fun.com

I could port the FPGAconf to Linux, but I don't have time right now, so please consider Linux unsupported.

You could do the programmnig yourself, it's not difficult, but some work nonetheless.
The boot-PROM is an M25P10 (equivalent to the Altera EPCS1) and the protocol is published in Altera's Cyclone datasheet or ST's datasheet.

The FPGAconfig programs runs in wine for me, if your looking for a quick way out. Can't get Altera to run though (not even text-mode), have you had any luck? Are there any other ways to get rbf-files then to use altera? What prevents me the most from playing more with my pluto (except maybe exams next week) is that I have to reboot into windows all the time.

No, you have to use the Altera software to create files for Altera FPGAs... same story for Xilinx.
Altera has a Linux version of their software, although not for free.
See http://www.fpga4fun.com/designsoftware.html

I read that you can get quartus to work in wine. You have to install it and then not run it before copying the filesystem and registry over to wine. Havn't had the time to try it.