If you want to do a true "clean" install, the only way to go is by doing it manually. No matter what migration option you select, your likely to get pref files or other things that come along during the install. Although moving licenses can be a pain, the only real issue is with high end apps like Adobe's Creative Suite which require you to de-activate on the old computer and then activate on the new computer. For most apps, they don't authenticate via a license server so you just need to type in the license key on the new machine without worrying about de-activating the license on the old machine.

If you do the install manually, installing Mail on your new machine (with all your messages and folders intact) is rather easy. Simply take your entire mail directory (USER/Library/Mail) on your old machine and drop it into the same location on your new machine. Do this before opening mail for the first time. The same method can be done for things like your iTunes library or iPhoto library.

Good luck! And with any migration, I would make sure to backup your computer to an external before you make the move.

Mike

When I got a new Mac I just used the migration tool and it worked perfectly. It works so well that I'm not really sure that my new system is "clean" in the way you are wanting. But I also like SuperDuper! which I used to make copies of my operating system. It's free (for the basics) and works great. If I were you and I wasn't sure, I would use SuperDuper! to make a clone of my new machine, then use the migration tool and if that didn't work right I could restore to the original system.