Time machine will transfer everything, as you left your system, good and bad included.
The best way to transfer over stuff if you are having issues with installed software is manually, which is not the easiest of tasks.
For instance, I did a clean install, and manually moved back items from my time machine backup, and it took me a few attempts, as far as finding all the related items to all the applications that I wanted to function as I left off.... ie bookmarks and add ons for browsers, song plays counts etc for itunes, mail, and the list goes on.
As I went to use certain applications, I still found a few items missing and had to read reports if available, or just try and locate certain things, as time consuming as it was at times.
However, after the many many hours that I put into this, all the glitches are gone from the OS and the apps

A clean install, followed by reinstalling all the software either from install discs, and/or fresh downloads directly from the sites is the best way to go as far quick and easy goes, and then transfering pic, documents, music, etc manually.
After that, you can always sort through the related files on your backup that you may really want.... such as anything related to itunes to have it identical to the way you left off.