Duplicate applications after using Migration Assistant

I'm posting this because I haven't seen this topic addressed yet regarding using Migration Assistant for transferring data from old G5 to new Mac Pro.
I used the Migration Assistant, which took hours to transfer data and stopped the first time due to a power backup overload. The second time I ran it, everything had transferred successfully, and I've been using my Mac Pro for almost two weeks now, with slight glitches that have been easily solved.
Here's my situation: In my Applications folder, there are a number of applications that have "(from old Mac)" as a suffix. Specifically, all of my Adobe Creative Suite applications have duplicates, as does Cocktail Extras, Corel Painter IX, DiskTracker (Mac OS X), Extensis Suitcase X1, Fetch 4.0.2, Finale 20045 and 2005b, and FontDoctor X for Macintosh.
Needless to say, I would like to recover the additional disk space that these duplicates are occupying, but is it okay to simply trash the ones that say "(from old Mac)", as I backed up my old G5 right before runnning the Migration Assistant, and I still have it sitting here, just in case something bad happens while I'm in the middle of a project? Or, should I trash the new ones? The Creative Suite apps have been activated on the Mac Pro, so I'm assuming that the "old Mac" ones could be deleted.
Anyone having any experience with this? I don't want to reinstall a lot of things unless I have to, as I will be upgrading a lot of the apps as soon as Intel-native versions are released, and things are working well so far.
Thanks for any advice you can give me.
2 x 3 GHz Dual-Core Intel Xeon   Mac OS X (10.4.8)   8 GB RAM
1.8 Mhz G5   Mac OS X (10.4.2)  

Yes, it's OK to trash them. You have transferred items that are from a PPC Mac to an Intel Mac that apparently had Intel versions of the same software already installed. You definitely do not want PPC versions (this does not apply to most Adobe software which is PPC-only.)
Unfortunately, Migration Assistant doesn't always know when not to transfer PPC software to an Intel Mac. This is especially a problem for the /Home/Library/ and /Library/ folders because MA may overwrite Intel components with PPC components. This can cause the Intel Mac to run slowly or not at all.
A Basic Guide for Migrating to Intel-Macs
If you are migrating a PowerPC system (G3, G4, or G5) to an Intel-Mac be careful what you migrate. Keep in mind that some items that may get transferred will not work on Intel machines and may end up causing your computer's operating system to malfunction.
Rosetta supports "software that runs on the PowerPC G3 or G4 processor that are built for Mac OS X". This excludes the items that are not universal binaries or simply will not work in Rosetta:
Classic Environment, and subsequently any Mac OS 9 or earlier applications
Screensavers written for the PowerPC
System Preference add-ons
All Unsanity Haxies
Browser and other plug-ins
Contextual Menu Items
Applications which specifically require the PowerPC G5
Kernel extensions
Java applications with JNI (PowerPC) libraries
See also What Can Be Translated by Rosetta.
In addition to the above you could also have problems with migrated cache files and/or cache files containing code that is incompatible.
If you migrate a user folder that contains any of these items, you may find that your Intel-Mac is malfunctioning. It would be wise to take care when migrating your systems from a PowerPC platform to an Intel-Mac platform to assure that you do not migrate these incompatible items.
If you have problems with applications not working, then completely uninstall said application and reinstall it from scratch. Take great care with Java applications and Java-based Peer-to-Peer applications. Many Java apps will not work on Intel-Macs as they are currently compiled. As of this time Limewire, Cabos, and Acquisition are available as universal binaries. Do not install browser plug-ins such as Flash or Shockwave from downloaded installers unless they are universal binaries. The version of OS X installed on your Intel-Mac comes with special compatible versions of Flash and Shockwave plug-ins for use with your browser.
The same problem will exist for any hardware drivers such as mouse software unless the drivers have been compiled as universal binaries. For third-party mice the current choices are USB Overdrive or SteerMouse. Contact the developer or manufacturer of your third-party mouse software to find out when a universal binary version will be available.
Also be careful with some backup utilities and third-party disk repair utilities. Disk Warrior (does not work), TechTool Pro (pre-4.5.1 versions do not work), SuperDuper (newest release works), and Drive Genius (untested) may not work properly on Intel-Macs. The same caution may apply to the many "maintenance" utilities that have not yet been converted to universal binaries.
Before migrating or installing software on your Intel-Mac check MacFixit's Rosetta Compatibility Index.
Additional links that will be helpful to new Intel-Mac users:
Intel In Macs
Apple Guide to Universal Applications
MacInTouch List of Compatible Universal Binaries
MacInTouch List of Rosetta Compatible Applications
MacUpdate List of Intel-Compatible Software
Because Migration Assistant isn't the ideal way to migrate from PowerPC to Intel Macs, using Target Disk Mode or copying the critical contents to CD and DVD or an external hard drive will work better when moving from PowerPC to Intel Macs.
Basically the instructions you should follow are:
1. Backup your data first. This is vitally important in case you make a mistake or there's some other problem.
2. Connect a Firewire cable between your old Mac and your new Intel Mac.
3. Startup your old Mac in Target Disk Mode.
4. Startup your new Mac for the first time, go through the setup and registration screens, but do NOT migrate data over. Get to your desktop on the new Mac without migrating any new data over.
4. Copy the following items from your old Mac to the new Mac:
In your /Home/ folder: Documents, Movies, Music, Pictures, and Sites folders.
In your /Home/Library/ folder:
/Home/Library/Application Support/AddressBook (copy the whole folder)
/Home/Library/Application Support/iCal (copy the whole folder)
Also in /Home/Library/Application Support (copy whatever else you need including folders for any third-party applications)
/Home/Library/Keychains (copy the whole folder)
/Home/Library/Mail (copy the whole folder)
/Home/Library/Preferences/com.apple.mail.plist (* This is a very important file which contains all email account settings and general mail preferences.)
/Home/Library/Preferences/ copy any preferences needed for third-party applications
/Home /Library/iTunes (copy the whole folder)
/Home /Library/Safari (copy the whole folder)
If you want cookies:
/Home/Library/Cookies/Cookies.plist
/Home/Library/Application Support/WebFoundation/HTTPCookies.plist
For Entourage users:
Entourage is in /Home/Documents/Microsoft User Data
Also in /Home/Library/Preferences/Microsoft
Credit goes to another forum user for this information.
If you need to transfer data for other applications please ask the vendor or ask in the Discussions where specific applications store their data.
5. Once you have transferred what you need restart the new Mac and test to make sure the contents are there for each of the applications.
Written by Kappy with additional contributions from a brody.
Unfortunately, if you find problems with your new computer it may be due to problems that arise when migrating from a PPC Mac to an Intel Mac using Migration Assistant. If this be the case your only recourse is to reinstall OS X. You should also reinstall your third-party software (or update it) to be sure you are using universal binary versions (if available.)
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