What _doesn't_ transfer to new machine via target disk?

Hello,
I upgraded from an old 867 tower to a Mac Pro and during installation I transferred my old disk's files via the firewire target disk mode. Everything seemed to transfer exactly, and most applications run fine.
Most.
Recently I found that Quicken couldn't find my current financial file, and I couldn't find it anywhere on the new machine, so I had to hook the old machine back up (glad I didn't erase the disk and sell it like I'd planned!) & transferred it manually. Now, Dreamweaver can't access my website at all, & I'm not sure what settings to even look at.
What doesn't get transferred when transferring files with this method? Where should I look (and for what) when I run across these oddball flukes?
Thanks in advance for any help with this admittedly ambiguous question.
Best,
Sean
Mac Pro 2.66 Mac OS X (10.4.6) PowerBook G4 667

I said before that if you transfer all your PPC applications as well as contents of the /Library/ and /System/ folders you will end up losing all the benefits of the Intel machine or worse you will have to reinstall OS X. PPC software is not intended to be used on Intel Macs, especially at the system level.
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
Written by Kappy with additional contributions from a brody.

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What _doesn't_ transfer to new machine via target disk?

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