Best method to go from iMac G4 to iMac G5 dual core

I'm struggling on how best to migrate from my old iMac G4 to a new iMac G5 dual core. I'd happily use the transfer data function at initial set up but wonder if I will be transferring "problems" from the old machine to the new. Is a clean install of all applications, preferences, data, etc. the best way to go? I have CDs for most of my applications, but not some of my shareware stuff. Are there any downsides to the transfer data route? Can I move applications for which I don't have a CD any other way?
iMac G4   Mac OS X (10.4.6)  

I would use the Migration Assistant and let it go at that for all my personal files. In the case of applications I would install them directly from the CD's rather than try and copy them. If I was using any applications that I had downloaded, I would just re download them.
Now, some things to make sure of.
1. Make sure that the software you install is compatible. Even if you just upgrading from a G-4 to a G-5 there are some applications which may need updating. If it is an Intel dual core then you need to check to see if a universal version is available or if it is something that will run under rosetta, if that solution works for you.
2. Make a complete backup of all your personal files and of course any itunes you have, anything in iPhoto that you have or anything else that cannot be replaced. Things can go wrong!! It may not be a big deal to lose a song you ripped from one of your CD's but it can be an issue if it was a song you purchased from iTunes Music Store so make a backup. If you use Quicken by all means back up your data files. If you use Entourage for mail make sure to back up its database.
If you have applications that you don't have the CD for you can try to copy them from one to the other but sometimes that does not work. There may be files installed for that application that you don't know about. All you can do is try.
Good Luck and I hope you enjoy your new Mac!!

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