The songs that defined the 90's were grunge. These songs didn't always chart like those acts that had developed a following in previous decades like Elton John, Billy Joel, Mariah Carey, etc.
These lists are always lame. I guess they had to put a Nirvana song on top, but you have to go way down the list to find another grunge song.
I’m wondering if there were even 100 good songs in the 1990s, let alone best songs.
However I've recently been re-immersing myself in the music and grunge was gigantic but really only for a few years, strictly speaking. Nirvana collapsed, Pearl Jam changed their sound, etc. After that we had brit-pop (Oasis) and trip-hop (Bjork, Portishead) and the rise of hip-hop and a lot of unusual mixes of genres (Pat Boone singing metal? Us3 putting out music that blended jazz and hop hop, etc). And you had stuff that stood on their own like Dave Matthews and Beck and NIN and others.
I Think the 90s was actually a really interesting era for music, now that I have some distance to re-evaluate it properly. Nothing like today, lots of new bands with totally unique sounds and experimentation with cross-genre work, pretty creative instead of the same song autotuned and overproduced over and over with every artist to the point of genericity.