I have Quartus II 7.0 running on a Gentoo Linux box using a stock 2.6.20 kernel. As stated by others, you may run into trouble using the USB Blaster, but that's only a permissions problem.
My system uses udev for hotplug devices, so I created the file "32-altera-rules" in the /etc/udev/rules.d directory. The file looks like this:
==== Cut here ====
# udev rules file for Altera USB programming devices (udev >= 0.98)
#
ACTION!="add", GOTO="altera_rules_end"
SUBSYSTEM!="usb_endpoint", GOTO="altera_rules_end"
ATTRS{idVendor}=="09fb", ATTRS{idProduct}=="6001", MODE="0666"
ATTRS{idVendor}=="09fb", ATTRS{idProduct}=="6002", MODE="0666"
ATTRS{idVendor}=="09fb", ATTRS{idProduct}=="6003", MODE="0666"
LABEL="altera_rules_end"
==== Cut here ====
I then found out that I also need to place a writable file called ".jtagd.conf" in my home directory for the whole thing to work, but after that things ran smoothly.
Best regards,
Ben