Mac Pro going extremely slow

Hello,

I have a Mac Pro v1.1 running Snow Leopard with 12 GB of Ram and one HD of 250GB

Suddenly it works very slow. All the applications I was using before are not running correctly. I clean installed Snow Leopard, I upgraded to Lion and then again downgraded to Snow Leopard, I removed some of the RAM modules and placed them back but still the problem is not solved, i also repaired disk permissions a milion times. Any suggestions on why this is happening? I also tried the same applications on my Macbook pro with 4GB of Ram and i5 processor and they work much better which doesnt make sense to me.

Thanks