I know I can make an easy transfer of everything using time machine, but I'm trying to transfer the minimum necessary to the new computer (applications I currently use, Aperture database, etc.) in order to keep the new machine as clean as possible, and avoid starting out with any legacy problems with permissions, etc.
Clearly, I can copy individual apps and databases to an external drive and then install them on the new machine, but I'm trying to find an easier way.
Best Answer
Have you looked at "Migration Assistant" in the Utilities directory (off Applications)? Note -- I haven't used it myself.
That utility should work over the network (so you don't need an external disk) and I think it gives you control over what gets transfered. It isn't whole disk but, like you want, user data and applications.
Note -- I tend to reinstall applications when moving to a new machine. Although a lot of applications for Mac OS X are self-contained (everything is in that application icon), there are some that install things in odd places on the hard drive and it can be a pain to track all those things down, or even to understand that something is missing (when all you get is a crash or weird error message).