[robespierre]

I would run 6.5.22 on all of those machines. It is the highest version supported on Indy or Indigo2, and will work fine on the Onyx 2 as well. Onyx 2 can use up to the latest IRIX release, 6.5.30, but I'm not aware of any specific benefit of doing that.
It's true that 5.3 and 6.2 can be faster, but the real difference that hits the most is the memory requirement. 5.3 or 6.2 can run comfortably in 256MB but you really want more than that for 6.5. The R4000 Indigo2 can use up to 384MB of main memory and the R10000 Indigo2 can use up to 1GB. The sticking point is that 5.3 and 6.2 were not universal releases. There were specific discs for different machines and configurations and it can be harder to find the precise disc required.