Migration Assistant vs Target Disk

Originally I came here because I am unable to get the two Migration Assistants to talk to each other over ethernet - or Airport. They just kept on "searching for other computers" endlessly until timing out....but - *Forget that for now* - I am waiting on getting a Firewire 800-400 adapter since my new Mini has a 800 port - and my iMac PPC G5 is a 400!
What I did find in reading threads is how problematic MA "might" be - and alternatives to it. So what I'm looking for are recommendations based on the following -
I have a huge number of applications on the G5 - a rough guess is 200+ and that 75% of them are Universal. I don't care about moving anything over other than applications. (Files can simply be brought over as needed by shared disk!) I don't care about user accounts (only me), settings, preferences or anything else at all - JUST APPS!
My biggest concern are licenses/installs. I'm not very organized on this point (thinking I would have no issues using MA) so some came by emails, phone, some are in a box, download documentation or manual and many I can't even remember how it came or what I did with them after I bought the apps. If I got a DMG/Install/MPKG/Zip/PKG. file for instance - chances are I installed and deleted it, rather than burning a disk for a hard backup and writing the S/N on the disk... (learned my lesson there).
Now I'm reading that some of my apps won't work via any type of transfer without chasing down the manufacturer for each one with endless nightmares of being put on hold forever! It could literally take months! This is more than a little disturbing as I was hoping I could just run MA, let it sit overnight and do it's thing and have all my tools ready to go.
I thought moving to an Intel box would make my life easier, but it's not right now! LOL
So now I'm just wondering what's the best approach in my situation?

It went fine using MA - everything appears to have moved over.
1. The "info" on apps no longer says if it's a PPC or Uni or anything - just "app"...kind of strange.
On my system older apps still have a "Kind" of things like "Application (PowerPC)" or "Application (Universal)".
Do I now need to do anything? Repair Permissions? I recently saw one thread when RP was causing someone major problems on a Mini!
Repairing permissions isn't the magic bullet that some fee it is. In particular, it won't do anything for non-Apple software.
So far the couple of apps that I have tried are DOA on the Intel box after a MA xfer...meaning the keys didn't come over.
Better than having to reinstall everything!

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