Migrating to new iMac, what does Migration Assistant actually migrate?
I've migrated between many macs over the years, and I've always found that the best way to do it, is manually. Normally I use a firewire cable (but you can also use WiFi, USB, external hard drive, dvd/cd, etc) to hook up the two computers, then just drag over files from one computer to the other.

Mostly everything the average user has on their mac will be found in their user folder (home folder). You can just drag/copy this entire folder over, or you can be more selective about which folders in your home folder you move (for instance, you may not want the Library folder). Then, anything outside of your home folder (Applications, for one) you can drag/copy over if you want.