I used to run separate Emacs instances on both Windows and Linux, but these days I settled for a different workflow. I keep my main Emacs running on my home Linux desktop. From other computers and locations, I just SSH to the desktop and run an Emacs frame in terminal mode (the command is just: emacsclient -t). Turns out, this is usable for about 95% of things I use Emacs for (the remaining 5% are when I need to view a picture or a PDF, which obviously won't show in terminal). Hell, if you configure your terminal/SSH client to run in 256-color mode, the resulting terminal Emacs will be nearly indistinguishable from the GUI one!
That's one of many hidden strengths of Emacs-based workflow - it works the same whether you're running in GUI mode, or connecting remotely with text terminal. That also means I can work on heavy projects from my underpowered 2-in-1 netbook :).
I have done this before but I like going one step further and running Emacs over X with xpra or similar. An annoyance with xpra in particular last I looked into it is that the protocol version has to be identical on all your machines or it just refuses to connect (it has no concept of forwards/backwards compat in the wire protocol), and debian/ubuntu package different versions, so you end up having to build it yourself locally everywhere.
That's one of many hidden strengths of Emacs-based workflow - it works the same whether you're running in GUI mode, or connecting remotely with text terminal. That also means I can work on heavy projects from my underpowered 2-in-1 netbook :).