Will reinstalling snow leopard overwrite applications?

Yesterday my Mac Pro refused to start up.

On the grey screen a "question mark folder" flashed up for less than a second, then the apple logo and then it went to a blue screen and stayed there with the spinning circle going round and round...

I booted from the Snow Leopard install disk (I was on 10.6.8) and ran disk utility. Verified and repaired the disk and permissions. When I tried to reboot from the startup disk the same blue screen issue happened.

Have also booted in single user mode and done fsck, have reset the pram and smc but nothing seems to work.

I feel like the only option is to reinstall snow leopard from the disk but I have a lot of applications on my Mac and I am wondering if these will be wiped when I reinstall or will they be left untouched? I'd just rather not have the hassle of dealing with deauthorizing software licences etc...

Also - any ideas of what has happened?

Any help much appreciated.

Many thanks,

David