Recently I tried compiling Eigensoft on my Ubuntu 10.10 Linux system running in Virtualbox and had no success. From comments on this blog post, it looks like the newer Ubuntu distros don't have the libg2c0 and related libraries (which were a part of the gcc3) and gcc4 uses gfortran instead. So it looks like Eigensoft won't be compatible with any of the newer Linux distros, at least without some major tweaking that I'm not prepared to bother with.
Ross Lazarus suggested in a comment to try Shellfish as an alternative. I was able to compile Shellfish without a problem on Ubuntu 10.10 but I haven't had a chance to try it out yet, nor make any comparisons with Eigensoft. The documentation on the website shows that it can directly utilize PLINK ped and map files, so this eliminates the burden of using a tool like PLATO to convert between formats.
Has anyone ever used Shellfish (or anything else besides Eigensoft) for PCA on GWAS or AIMs data?
EDIT 2011-02-14: A tip of the hat to Mike Baldwin for pointing out to me that Eigensoft version 4 is now available on Alkes Price's website. A Google search always puts you at Eigensoft version 3 from the Reich lab software page, which is the old version that doesn't play well with newer Linux distros. I had no problem using Eigensoft 4 on my Ubuntu 10.10 system.