Restore in place feature?  OSX.6.3 running kinda rough

I think it is time to revitalize my OS, but I have not seen a clear route to "restore in place" on my Snow Leopard DVD. Any advice please? Mostly I am getting lots of quits in Photoshop CS5 products, 64 bit mode, tho I used to not have such problems with CS5 products in 64 bit mode.
I have run permissions regularly, scripts.
I have onyx but there are cleanings and sweeps I'm afraid to do.
I'm not excited about a clean install because reloading all my programs really takes a long time.
I had disk warrior and tech tool for previous systems, but I was hoping to side step the need for these on Show Leopard.
By the way, isn't OSX supposed to start up real fast? Sometimes I get 2 minutes+.

I do use SD. Can I just recover what is damaged with SD? Problem is, I think the damage is cloned too.
And actually I cannot access my Time Machine cuz the drivers for those eSATA back up drives are what bungled my system. But if I could, would I just recover "system"?

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