In 2011, CT600 worked on Linux if you followed some complicated steps to manually import the SSL certificates from Companies House and HMRC websites. In 2012, it broke, with no amount of manual importing resolving the error
SSL Error!!!. Please install the CA Certificate(s) for SSL communication. If certificate resides on local disk, try "acroread -installCertificate [-PEM|-DER] [pathname]" on the command line. If certificate resides on the server, try "acroread -installCertificate xmlgw.companieshouse.gov.uk 443" on command line.
HMRC helpdesk were clueless, sending me back the forum link I had sent them, and asking me to make sure that I was using Adobe Reader. The good news is that I attempted to use it again yesterday, and it all just worked without any fiddling. I used Adobe Reader 9.5.3 32-bit on Ubuntu 12.10 64-bit. Just follow HMRC’s instuctions on fiddling with Adobe Reader’s security settings, and all should be well.
Also see my post on Adobe Reader on 64-bit Linux.