Need help about MoBo support



They both perform about the same, so the difference is not noticeable.
By the way the Q9650 goes on LGA775, the socket on the MSI MS 7366, but the Xeon 5460 goes on a LGA771 , which is a different socket.
 
Running an LGA771 Xeon on an LGA775 motherboard is a fairly complex modification. Many motherboards don't support it at all.
https://www.delidded.com/lga-771-to-775-adapter/
1- You need a compatible chipset on the motherboard, and then there may be other issues anyway.
2- The LGA775 socket needs to be modified to fit, or the CPU notched to match the socket.
3- There is an elctrical tape adapter that's required to convert the dual CPU back to single CPU configuration.
4- Then the BIOS usually needs to have the Xeon microcode installed so it can recognize the CPU correctly.
Some of the Xeons are clocked slightly faster than the Q9650 3GHz, X5460 3.16GHz, X5470 3.33Ghz.
But any unlocked MB, or MB that supports an unlocked CPU (QX9650) can easily exceed those speeds.
 

On everyday tasks (web browsing, word processing, etc) you won't see a difference in performance.
If you could get the Q9650 for $20 or less go for it.
Depending on the cooler you have you might need to upgrade it, since the Q9650 produce more heat.