guitarix is a virtual guitar amplifier for Linux running on Jack Audio Connection Kit. It is free as in speech and free as in beer. The available source code allows you to build it on other UNIX-like systems too, namely BSD and MacOSX.
guitarix takes the signal from your guitar as any real amp would do: as a mono-signal from your sound card. The input is processed by a main amp and a rack-section. Both can be routed separately and deliver a processed stereo-signal via Jack. You may fill the rack with effects from more than 25 built-in modules from a simple noise gate to brain-slashing modulation f/x stuff like flanger, phaser or auto-wah.