Operations like these have always been dicey since 3rd Party programs can scatter their settings where ever they wish. So hunting down those settings without the use of the program's own installer is tricky.
An interesting but not bulletproof method I've used a few times is the Windows Easy Transfer, which is like a little brother of the "more complicated to setup" Microsoft USMT tool.
There are other options like the popular LapLink.
The How-To Geek has typed a good guide to Windows Easy Transfer. I copied the instructions without screenshots.
Migrate XP to Windows 7 with Easy Transfer Over the Network
If you get a new computer with Windows 7 and your current machine is
running XP, the thought of transferring your files and settings can be
quite daunting. Microsoft has created a program called Windows Easy
Transfer that is already included in Vista and can be download for XP
and 2000. Here we will take a look at the process of using it to
transfer files and settings from an XP machine to the new Windows 7.
Starting with the Windows 7 machine open the Start menu and go to
Getting Started and under Tasks click “Transfer your files”.
Click through the welcome screen and choose the method for
transferring the data…in this demo we’ll use a network connection.
Next select that this is the new computer.
The next screen click on “I need to install it now”.
Choose a network or external drive to install the latest version of
Easy Transfer. If you use a flash drive a freshly formatted one is
recommended as it installs Windows Easy Transfer like a portable app
which runs directly from the drive.
The next screen prompts you to go to the old computer, start up Easy
Transfer and run through the wizard until you get a transfer key.
Now on the XP machine run Easy Transfer from you flash drive.
A progress screen will be displayed while it starts up and produces
the transfer key.
Enter in the transfer key from the old machine on the new Windows 7
and hit Next.
It will scan the old computer and determine what can and cannot be
transferred over.
When done you can select the general settings and files from all the
accounts on the machine.
Click on Advanced to get a detailed explorer view so you can
specifically select what to transfer over. When you’ve decided what
to transfer then click Save and then transfer it over. The amount of
time it takes will depend on how much you’re transferring, speed of
the network, etc.
When it is all complete you can view the transfer and program report
which shows the files and settings transferred and also what programs
are or are not compatible with Windows 7.
To finish the process a Restart is required.
Windows Easy Transfer can be downloaded for XP and Windows 2000 from
their site but you might want to use the process shown above as it
supplies the latest version of Windows Easy Transfer. We ran into a
problem with running the downloaded version which was installed on XP
and was not compatible with the Windows 7 version.
Not all programs and settings are going to transfer to your new OS but
this definitely makes it easier
Best Answer
What kills most drive transfers is the disk driver. Sysprep is designed to remove most drivers which allows you to boot to an installation environment and redetect the drivers. As others stated, you need configure the Hard drive settings in the BIOS of the new system to match your old one (AHCI, RAID, or IDE). I'd grab a secondary hard drive and make clone of the current disk in case something goes horribly wrong. There are a ton of disk mirroring solutions out there so pick your preferred flavor. (I use easeus disk mirror)
From your description, you may need to reorganize how you are saving your data. If you are concerned about data loss when a workstation goes down, you are doing it wrong. Your data should be arranged in a way that it is either stored on redundant network locations, or have automatic backups to a secondary storage device. There are hundreds of backup schemes out there and a ton of tools to help set this up. The investment of a little time and hardware can save a ton of time rebuilding lost files.
Finally, you might think about building some automated installation scripts. Most programs come with a silent installer option to make doing this a breeze. While the time investment to set this up is longer than a simple install, it makes the chore of reinstalling an easy one. Being able to rebuild a system quickly is really useful when you have a team all using the same software.
Food for thought, good luck.