I'll put together some sort of "Inside the Numbers" post on the site or in the forums after we put up #2/#1. I will say that #2 and #1 were the clear favorites as the staff votes came in and were neck and neck throughout.
Link to the Past was a clear #3, but I think the one that hurt it, at least in our staff voting, is that it would be consistently #3/4 on people's lists, but wasn't at the top as consistently as the games above it. By comparison, out of our 23 voters, LTTP appeared as #1 3 times, but our top 2 combined for 12 first place votes.
For #4-#6, it was very even throughout the voting, though a little bit of late love for Link's Awakening made the difference greater. Majora's and Skyward would flip-flop with pretty much every list I got from staffers.
And for the record, one trolling staffer voted for Shadow of the Colossus.