From Golems Universal Constructor
Currently, Golems' linux support is mainly focused around Ubuntu or Ubuntu variants like Linux Mint. Golems still runs fine run on other Linux systems providing you have Java v1.5 or v1.6 (v1.6 is recommended though), and the proper video drivers for your graphics card. If you are logged in using the root account (depending on your preferences or linux distro), you can ignore the sudo command when it precedes other commands.
Unfortunately, there are a few known problems which need workarounds in order for Golems to function properly.
v0.54.x Java Workaround
As of v0.54.5, Golems now supports 64-bit.
In v0.54.3 and v0.54.4 there is a problem with running Golems on 64-bit machines with 64-bit java. In order to run this version you must use 32-bit Java libraries. Instructions for Ubuntu are as follows, (other distros should be similar):
1.) Install 32-bit libraries:
sudo apt-get install ia32-java-6-sun
2.) Find where the binaries are located:
sudo update-java-alternatives -l
Copy the location of the ia32-java-6-sun (It should be located in /usr/lib/jvm/ia32-java-6-sun).
3.) Go to the folder where you installed Golems and edit java_home. On the first line, add the location which step 2 provided you.:
Voila, golems should now run in 32 bit mode!
Note: If this forces Java to run in 32-bit for all other applications, set your default Java to 64-bit:
sudo update-java-alternatives -l (copy the path to your 64-bit Java) sudo update-java-alternatives -s <path to 64-bit>
You only need to be sure that .../Golems/java_home is modified properly to use 32-bit.
v0.54.2 (and lower) Issues
Due to a problem with the physics engine, there were some major issues with native Linux support. The only way to ensure the game would run as expected was with WINE. If you must use an older version of Golems, then it is recommended running it under WINE.
1.) Download WINE here: 
2.) Follow the instructions for your distribution/flavour of linux.
3.) Download the Windows version of Java. Make sure you get the OFFLINE INSTALLER (The online installer didn't work for me, if you can get it to work, please let us know on the forums in this thread).
4.) In your file manager, right click the Java installer .exe -> Open with "Wine Windows Program Loader". If this is not present in your file manager's menu, try running wine from the command line in the directory you downloaded the file to. Something like this should work:
:~$ wine jre-6u14-windows-i586-s.exe
(please let me know if it doesn't!).
5.) Get the Windows version of Golems from the download page and run it the same way you ran the Java installer in step 4.
Everything should now run smoothly!
Please report all bugs or problems in the forums.