The common thread is the way they were viewed and are currently viwed looking back (we are granted this hindsite in the conversation to be able to look back, which is nice) and what they had accomplished up until the moments when the respective fighters we're talking about came along and toppled them.
Fedor, if I am not mistaken, was considered above both those guys when they fought -Nog I'm fuzzy on at that point so, I'll leave that to you guys.
Hughes and Penn no question were already considered the best and were on runs supporting that claim when GSP came along and scored victories over them -Fedor was above both Cro-Cop and Nog in the minds of many at the points they met up (again, I might be missing a ranking here with Nog, so I'll allow for that)
I know its a small discrepancy in a way, so this all comes full circle and back to it being subjective and I'll leave it at this: to me (just my opinion of course) GSP's victories over Penn and Hughes in accordance to when they occurred, are more impressive to me than Fedors victories over Nog and Cro-Cop. I know this won't be popular, but thats fine, thats why we all have our own opinions that allow us to have these types of discussions.