Make sure all your computers have the same major version (all 23 or all 24; I recommend 24 as it actually has a package manager). OSX was for several years a problem for emacs as there were two or three incompatible ports that did things differently; it's probably gotten better over time.

As preavy said, the rest can be handled by checking the OS type, machine name, user name, etc in your init files (they're not just config files, they're emacs lisp programs that get run during startup).

I keep mine in a git repository to make syncing the changes over time easier.

I have my .emacs.d symlinked to a folder in Dropbox. So to set up on a new machine I just have to install Dropbox and make a new symlink.

This also worked for me in Ubuntu.

I was concerned when package management came in as a lot more stuff seems to get downloaded, but it just seems to look after itself.