1. Basically our methodology was to listen to every song from all notable N64 games, give each song a score from 1-10, average our scores - giving us an initial ranking - and then debates, debates, debates over song order and song inclusion. We were very thorough and methodical, so this whole process took nearly a year to complete (!). We also made an effort to include as many games as possible, so long as their inclusion could be justified.
2. We didn't poll, but as you can see at the end of the video I did data capture from other music ranking lists to see what the general consensus was. This influenced us to an extent, but ultimately we favored our own "science". The masses are often wrong, for example almost zero lists had any Jet Force Gemini songs!
3. I did some data capture on youtube view counts for the top songs to get a sense of popularity. It's tough, for example Song of Storms from Ocarina of Time is hugely popular, but we didn't feel it was worthy of making the top 100. But at the same time, if we were borderline on a song, but the song was popular, that usually made the difference between either inclusion or upping the rank.
Hope that helps!