ise 4.2
Xilinx ise 4.2 does not have any linux version, but you can run it's main executables such as, par , ngdbuild , map under linux, using wine. Even it seems that Xilinx's new ise 5.1 does not have a linux version yet.
As you know, running a windows program such as par.exe under linux, although possible, will consume a lot of time, and is slow, so you can not do big implementations under linux for xilinx FPGA.
However, Altera has ported it's quartus development tool to linux completely, when you run it under linux you will see a program just the same as it's windows version. I think there is now a technique that lets designers to compile their windows written code for linux, with out any big change.