I had the exact problem (lost file associations, exes would launch "open with" box, etc) and finally found the mix of things to resolve it (after days of searching and trying everything).
I downloaded Malwarebytes' Anti-Malware at http://www.malwarebytes.org/ (free). It found "Hijacked.exeFile" (virus) and cleaned it.
Then I followed the following from another forum:
http://social.answers.microsoft.com/Forums/en-US/vistaprograms/thread/ba8cab9b-29e1-49cd-adf7-22f7e0999060
Fix the registry...
1. Type command in the RUN dialog box to open Command Prompt
2. When Command Prompt is up, type cd \windows
3. Type regedit to open up the Registries.
4. Expand HKEY_CLASSES_ROOT and find the folder of .exe
5. Without expanding it, on the main .exe folder, Right-click (Default) and Modify . Change the Value Data to exefile [MINE SAID SECFILE]
6. Now in the same HKEY_CLASSES_ROOT find the folder of exefile and Right-click (Default) and Modify . Change the Value Data to "%1" %* [MINE SAID APPLICATION]
7. Lastly expand exefile , expand shell , expand open , click on the command folder, Right-click (Default) and Modify . Change the Value Data to "%1" %* [MINE ALREADY SAID THIS. DIDN'T HAVE TO CHANGE]
8. Close Regedit and Restart the computer. When restarted, EXE files should not prompt you to choose a program to run it now and load correctly.
Once these steps have been completed scan your laptop for any viruses/malware/trojans.