I remember once I wanted to e-mail a perl script I had written home to myself so I could work on it some more. Hotmail ate it as a virus so I renamed it .txt and all was well.

As for how clever virus scanners are at detecting minor changes such as adding pointless loops or whatever to change appearance but not function, guess that depends on how smart the programmers are at the AV company in question and how smart the virus writers are. I do know I usually end up disabling the heuristic detection since otherwise it starts flagging everything as a virus.