In regards to installed programs (or applications) a change in Windows that occurred in 1995 changed how programs are installed and the change meant we can't easily transfer programs from one PC to another or from one OS install to another.
-> As you discovered, we can often remove the virus or pests but the repair of the damage is never a sure thing. That's why you read so much about backup copies of what you can't lose.
Bob
Long story, so bear with me. Got some type of virus on my XP machine (dell Dimension) which when the machine booted, a pop up screen would appear and I couldn't get rid of it or run any other program.
After trying safe mode and few other things I decided to try a Windows repair with my Dell OEM disk. Well, it did something and went to reboot and now I get an error that the hall.dll file is corrupt and needs to be reloaded.
Tried to do another repair but this time it appears to have created another instance of XP on my computer. When I reboot, I have to select between the two options, the forst one continuing to give me the dll error and the second booting up completely. However, the second instance appears as a new installation and is not connected to any of my existing "accounts". While I can get to the actual files I that were one the system, I can't run any of the programs as it tells me I must run set-up as the program was not set up for this "account"
Is there a way to access these programs without a re-install of each program? A way to delete or repair the initial windows selection that gives me the dll error?
Using the second instance I was able to run Malware bytes which appears to have eliminated the virus out of the "start" files for each of the users that were set up on the machine prior to this incident

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic