Why change machines when at your desk versus elsewhere? That sounds like an 'rsync' accident waiting to happen.
I've been using the first generation 11.6" Air which replaced a unibody 15". Other than FreeBSD and Linux servers racked elsewhere, this Air is my "everything" machine.
My tricks for the smaller screen:
Keep windows overlapping with just enough visible underneath to indicate status, and of course set the Dock to auto-hide. e.g., Mail window is on far right with little more than the scroll bar showing, so I can still see whether the horizontal cursor/bar is at bottom of that window or not, which indicates new mail. Of course, when I'm deep into code-mode, I don't want the distraction of email anyway until I come up to breathe, so it's one less distraction.
Likewise for Terminal. I have less than one row of text visible underneath Emacs, VMware and browsers. This is just enough to see if a background compilation or other task is still running. Again, like email-- one less distraction unless and until I want to be aware of it.
In Emacs, I'm using my own build of 24.0.50 with 185x46 character resolution and make heavy use of 'split-window-horizontally instead of 'split-window-vertically which I used predominantly on earlier machines since 1989.