To clean up some problems you may need to do an archive and install from your install CD. When you have the Apple Store do it they will frequently NOT select "preserve your user and network settings". The old ones will be saved in a Previous System folder on your hard disk. This may fix problems caused by things in your user Library or Library/Preferences, but can cause other problems (e.g. loss of your bookmarks, registration serial #, so your application will not run or default to a demo version). Some of the things I needed to restore are listed below.
When things are working you can remove the Previous System folder but one user reported a problem where an application was using the preference in the Previous system folder because it was smart enough to know it was moved there and deleting it created a problem, so I would create a copy of the user library in the previous system before on an external disk before deleting it.
See: About the Archive and Install feature at support.apple.com/kb/HT1710

One of the forums also said some applications (It didn't identify which ones) may need to be reinstalled even though they have universal binaries, because the install process recognizes an Intel Mac and does something differently. I couldn't find any confirmation of this.

You could Restore your whole user library:
(But this may copy the thing(s) that were causing the problem.
Copy:
From Macintosh HD/Previous Systems/20xx-...../Users/[ID]/Library
To ~/Library  where ~ is your home directory Macintosh HD/Users/[ID]

Note: Some things may be stored in the Shared folder under Users

Restore Individual Library Items:
Safari:
 ~/Library/Safari folder
 ~/Library/Preferences/com.apple.Safari.RSS.plist
             com.apple.Safari.plist
 Firefox:            
 ~/Library/Application Support/Firefox/Profiles/xxxxxx.default (folder)
   xxxxxx is a random number which may be different than your backed up files
   Either copy the contents of xxxxxx.default from the backup to the new folder
   or copy the backed up xxxxxx.default and change 
   ~/Library/Application Support/Firefox/Profiles.ini to point to it.
   ~/Library/Application Support/Mozilla

Stickies
  ~/Library/StickiesDatabase
  ~/Library/Preferences/com.apple.Stickies.plist
  ~/Documents/Stickies/
KeyChain:
   ~/Library/Preferences/com.apple.keychainaccess.plist
   ~/Library/Keychains/
    
 Adobe:
    Delete all adobe applications in your system and utilities folder
    Download and Run the CS3Clean Script (even if you only PS Elements and not CS3)
    at https://www.adobe.com/support/contact/cs3clean.html
    Select level 3 (not in list) and run it twice
    Select level 4 (not in list and run it twice
    Re-install all Adobe apps (Reader, Flash, Photoshop, ...)
    Photoshop elements go to Help > registration
    and input your name and serial # again.

Canon Scanner:
  /Users/Shared/CanoScan LiDE ...
  
Canvas
    ~/Library/Preferences/ADCsystems/
    ~/Library/Preferences/CanvasX.reg
    ~/Library/Preferences/com.acdsystems.canvas.ten.plist
    ~/Library/Frameworks/
    It still would not pick up my registration/serial # and ran as a demo.
    In Canvas, open a new document. Then go to Help | License manager.
    Select a product that contains a trial version status.
    Click Enter License Code. 
    
 BBedit:
    ~/Library/Preferences/com.barebones.bbedit.plist
    ~/Library/Preferences/BBEdit Preferences/ (folder)
    ~/Library/Preferences/com.barebones.bbedit.PreferenceData/ (folder)
   Note: You seem to have to restart before opening bbedit after installing
   "Grep Patterns.xml" in the above folder or it will revert back to the
   default.
Fetch:
  ~/Library/Preferences/com.fetchsoftworks.Fetch.plist
  ~/Library/Preferences/com.fetchsoftworks.Fetch.Shortcuts.plist
  
You may have to run Repair Permissions in Disk Utility after copying.

Others in Preferences
com.apple.BezelServices.plist
com.apple.dock.db
com.apple.dock.plist
com.apple.finder.plist
com.apple.internetconfigpriv.plist
com.apple.java.JavaPreferences.plist
com.apple.LaunchServices.QuarantineEvents
com.apple.MenuBarClock.plist
com.apple.PubSubAgent.plist
com.apple.QuickLookDaemon.plist
com.apple.quicktime.plugin.preferences.plist
com.apple.recentitems.plist
com.apple.sidebarlists.plist
com.apple.spotlight.plist
com.apple.systempreferences.plist
com.apple.systemuiserver.plist
com.apple.universalaccess.plist
loginwindow.plist
Macromedia
QuickTime Preferences


New:
com.apple.AddressBook.abd.plist
com.apple.AddressBook.plist
com.apple.BezelServices.plist
com.apple.dock.db
com.apple.frontrow.plist
com.apple.help.plist
com.apple.internetconfig.plist
com.apple.internetconfigpriv.plist
com.apple.java.JavaPreferences.plist
com.apple.keychainaccess.plist
com.apple.LaunchServices.plist
com.apple.LaunchServices.QuarantineEvents
com.apple.mail.plist
com.apple.MenuBarClock.plist
com.apple.PreferenceSync.plist
com.apple.Preview.bookmarks.plist
com.apple.Preview.plist
com.apple.print.custompresets.plist
com.apple.print.PrinterProxy.plist
com.apple.print.PrintingPrefs.plist
com.apple.PubSubAgent.plist
com.apple.QuickLookDaemon.plist
com.apple.quicktime.plugin.preferences.plist
com.apple.quicktimeplayer.plist
com.apple.recentitems.plist
com.apple.Safari.plist
com.apple.Safari.RSS.plist
com.apple.sidebarlists.plist
com.apple.SoftwareUpdate.plist
com.apple.spotlight.plist
com.apple.systempreferences.plist
com.apple.systemuiserver.plist
com.apple.Terminal.plist
com.apple.universalaccess.plist
com.barebones.bbedit.plist
com.barebones.bbedit.PreferenceData
com.fetchsoftworks.Fetch.plist
com.fetchsoftworks.Fetch.Shortcuts.plist
com.lemkesoft.graphicconverter.intel.plist
com.lemkesoft.graphicconverter.plist
com.microsoft.autoupdate.plist
com.microsoft.Excel.plist
com.microsoft.OfficeNotifications.plist
com.microsoft.PowerPoint.plist
com.palm.desktop.plist
Explorer
e Cache
iCalExternalSync.plist
loginwindow.plist
Macromedia
Microsoft
net.telestream.wmv.plist
OfficeSync Prefs
org.mozilla.firefox.plist
Palm Desktop Info
QuickTime Preferences
User Data…TF5801079

last updated 6 Feb 2009