I have a laptop which is sort of my main machine, primarily because it is what I use the most because I take it to school. It runs Arch Linux. I also have a desktop which is kind of my gaming computer, which is running Windows 7 and dual-booting Arch Linux.

I use github for keeping my dotfiles in sync, and my desktop and laptop almost work identically. There are differences between desktops and laptops, however, which is why I have two branches -- one for my laptop and one for my desktop. I will then just cherry-pick commits which apply to both branches.

For syncing stuff that doesn't necessarily belong under version control, I use dropbox. All of my code(some of which is under version control, but you can sync that with dropbox), my university stuff, and all sorts of other crap is synced using dropbox. This makes the whole sync process feel mostly transparent. My favorite robot overlord, Google, also takes care of syncing bookmarks and history and such across sessions because I use Google Chrome.

The only downside of maintaining multiple machines is the occasional effort to keep track of the difference between the dotfiles from machine to machine as well as dropbox being somewhat slow to sync at times, and I feel that the linux implementation of Dropbox is rather prone to bugs(hangs, idle spin eating cpu and such).