I'm hoping to obtain a new Mac mini soon and I'll be using that as my primary machine at home.  I'm curious about the transfer of files from one machine to the other.  The way I see it I've got three options.  Use migration assistant, restore from a Time Machine backup, or just re-install everything (which isn't really that much: Sib6, VDL, iWork, etc.)

Any suggestions on any of those three methods? 

I recently updated my macbook HD and replaced my optical drive with an SSD.  Prior to installing both drives I made sure to back up my computers HD via timemachine so that restoring the new HD to the previous HD settings and applications would be simple.

I was thoroughly impressed with the simplicity and speed of this process.  Everything loaded up just fine (with the exception of a couple VDL2.5 .nkx files being relocated).  I would highly suggest that you use timemachine and upon installing the new drive, select restore system to a timemachine backup.  I do believe that there is a way to go in an manually select the programs, apps, folders ect...that you want to load to your new system, if you don't want everything on your new HD.  This shouldn't take long at all.

What about software registrations?  Did all those transfer as well?  How did that work?

Yes sir, all of the registrations and licensing transferred over just fine.  However, a couple sibelius/vd2.5 .nkx files were misplaced, I just had to relocate them and drag them to the correct folder.  I wasn't asked for any License's, but I am not sure if this is true in all situations.  

Excellent.  Thanks!