Not exactly sure what the newest Tour OS is but the OS5's have been out for a long time for the Tour. Bell still doesn't offer the official OS but ityou can get the OS from other carriers if you like or just used a leaked version. It will not mess with your apps it should transfer over without a problem if you use Viigo you will just have to login to your account to reload everything you customized.
You shouldn't really notice much of a difference besides maybe quicker or even better or worse battery. It varies from each OS.
If you do find the OS you would like to update with all you need to do is:
1) Download the OS and install on your pc.
2) Ensure no other Blackberry OS version is on your pc besides what you just installed.
3) Go to DM and back up your files.
4) Close DM and Go to: C:/ > Program Files > Common Files > Research in Motion > apploader
5) Delete vendor.xml
6) Run apploader.exe
After it has been completed. Ensure everything was restored if not go into DM and restore you back file.
The update process can take anywhere from 20 minutes to hour so be patient
