There are a number of functions that I have come across that only work on the linux version of emacs. I can't remember any off the top of my head though.

Are you comparing Gnu Emacs on Linux and XEmacs on Windows? I found Gnu Emacs so ugly and alien on Windows and XEmacs so lacking in extension support that I gave up on both. Also, it's annoying to switch back and forth between Gnu Emacs and XEmacs. Therefore, my IDE on Windows is Putty. I log into a Linux box and connect to one of my long-running Screen sessions so I can use a decent Emacs :-)