I migrated all my old stuff from a G4 iMac to an iMac G5 so not exactly the same thing as you are wondering about. But, nonetheless, looking back there are a few things I would avoid knowing what I know now...
I asked for all my stuff to be migrated to the new iMac. Mistake because some of those apps didn't work on Tiger (my old iMac had a Panther system). Not only that but it brought in a lot of orphaned files from apps I had previously installed and gotten rid of, so my Preferences folder and Application Support folder was full of these.
I should have asked to only migrate my settings as I really really really hate, for instance, setting up my email accounts, ISP and the like. That would have made for a much cleaner system to begin with. What I did eventually was I sat down and cleared all the old stuff that didn't work in Tiger, tried to delete the old orphaned Application Support folders/files and pref files.
So before you do a mass migration of all your data, make sure you choose the right setting for this procedure. I gather you are migrating from a Tiger system to a Tiger system so apps not working right will be at a minimum in your case: you will only need to worry about the ones that don't play nice with Rosetta.