We know apps don't move so well so let's exclude those. Why not use the Migration assistant noted at http://support.apple.com/kb/HT4413
I read it notes use of the machine to machine as well as Time machine.
Bob
I am buying a new Mac mini and want to get it running just like my old MacBook Pro. I make backups using Time Machine to an external hd.
I can't quite get my head around how to transfer/migrate my old mac to the new one with my Time Machine backup.
I get how to recuperate files, photos, etc. but can't quite see how to copy everything to my new machine.
I am running the latest Mountain Lion.
I would really appreciate it if someone could explain the process to me.
I realize this is pretty basic. I am a good cook but my computer skills leave a little be desired!!!
Thanks.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic