It proved to be harder than I thought and I still might change it if I remember a video I might have forgotten. My Top 3 is pretty solid, but the rest may change. I limited the number of MJ entries because without that MJ could have easily occupied most spots in the Top 10 and I don't think that's just my bias. Actually, my search for videos I could add only confirmed that in me. It would have been easier to find more MJ videos to fill the spots... Music videos is an area where he is indeed head and shoulders above everyone else.
1. MJ - Smooth Criminal
THE best music video of all times, IMO. I love everything about it. The music, the choreography, the cinematography, the nod to old Hollywood/Fred Astaire (inspired without being a copy cat). Perfection.
2. MJ - Thriller
I wouldn't complain if on a mainstream top list it would be #1, it would absolutely deserve that spot, although I think it is not MJ's best video. I am not even completely certain it is his #2. I personally probably prefer Bad, Beat It and Remember the Time. But it is definitely the most iconic and the most influential. It broke down racial barriers, it gave MTV its highest ratings, it was pioneering, it is the first music video ever inducted into the US National Film Registry. It's culturally probably his most significant music video, so it had to be here.
3. A-ha - Take on Me
I believe this is another video that would feature in a lot of people's Top 10s. It's very creative, unique and stands the test of time.
4. Pearl Jam - Jeremy
I surprised even myself with this one when it came to mind. I'm not really a grunge fan, but this song, the genre and the video work very well together here.
5. Fatboy Slim - Right Here Right Now
I love it how evolution could be the topic of a music video. Really creative and memorable video.
6. Madonna - Like A Prayer
Madonna was another huge artist of the MTV era and I was thinking about which video to include by her. In terms of cinematography Frozen is a visually beautiful video, but every other aspect of it is boring to me, unfortunately (boring song and other than being nicely photographed, boring video too). Vouge might be slightly more iconic than Like A Prayer, but I don't think Like a Prayer is much behind and the song is much better to me, so that's why I chose this one.
7. Sinead O'Connor - Nothing Compares 2 U
It is my only Prince entry on this list, with a twist because I took Sinead's version. Like said Prince wasn't really a great video artist, but I always loved what Sinead did with his song and I think a lot of it is thanks to this video. I think the video carried her version as much as the song itself. It's a very simple video, but I just love the emotions expressed on her face - I think that exactly is what elevated this song to the hit it was in her version.
8. Peter Gabriel - Sledgehammer
Nothing much to add to what was already said. Probably one of those videos that has a safe spot in any best ever music videos list's Top 10 and I acknowledge its pioneering quality. And I agree that Leave Me Alone is a bit reminiscent of it.
9. Run DMC - It's Like That
I don't know I just always loved the dance in this video. LOL.
10. Beastie Boys - Sabotage
It was played to death on 90s MTV and it really is a great video IMO.
Honorable mentions:
Janet Jackson - Rhythm Nation
I tried to include Janet in my Top 10 and if I had to pick a video by her it should be RN in terms of iconic status, but re-watching it now somehow it didn't impress me that much because I felt the choreography is a bit slow if it makes sense. Janet's moves in The Knowledge are much more dynamic, but that one is hardly even a song - it's more like the Panther Dance at the end of Black or White (and who knows, MJ might have taken the inspiration from The Knowledge to include such an angry, visceral dance sequence at end of BoW).
To be honest of Janet's videos I enjoy Love Will Never Do (Without You) more than RN, but then I don't feel Love Will Never is iconic enough to include in my Top 10.
Britney Spears - Baby One More Time
Say what you want about Britney and manufactured teen pop, but this is a great, iconic video, plus a catchy tune.
Pet Shop Boys - Heart, Domino Dancing, Being Boring
When I first started paying attention to pop music MJ was my #1 favorite from the start, but at the time Pet Shop Boys were my #2. Not least because I loved the horror themed Heart video. And Domino Dancing still take me back to that late 80s mood. A latter fave video by them is the beautifully photographed Being Boring (great song too).
Queen - I Want to Break Free
Queen weren't really a big music video band, but I loved this one for the self irony and humor.
Dire Straits - Money For Nothing
"I want my MTV". Need I say more?
As to what matters more when we rate music videos: the song or the visuals, I'd say both and I find myself deciding about it on a case-to-case basis. For example, in case of Thriller obviously I considered more the video, as I don't think the song is among MJ's very best. But I side-eyed Rolling Stone (or was it Billboard?) when the only MJ video they put in their Top 100 was Billie Jean (at No. 10, I believe), because while one might have a good argument for it being MJ's best, and definitely most iconic song, but when we are talking about music videos, he has countless of videos that deserved to be more in the Top 10 than Billie Jean and they weren't even put in the Top 100 which is absurd. (Although I felt RS/BB deliberately ignored those better videos, because they knew if they acknowledged something like Thriller or SC they should have put it at #1 and they just didn't want an MJ video to win it.)
So yeah, the "best video" doesn't mean "best song" to me, on the other hand the music did factor somewhat in my choices. For example in picking Like a Prayer from Madonna instead of, Vouge. At other times, my dislike for a certain music lead to dismissing an objectively creative/nice video. Eg. Björk videos. I acknowledge her creativity and uniqueness both in music and videos, but I just can't get into her music and because of that I don't enjoy Björk videos no matter how nicely they are done.
On the other hand like I said I'm no huge fan of Fatboy Slim's music, but it doesn't bother me either, it's more in the "okay" category to me, so I didn't dismiss the video in that case just because I don't otherwise listen to that type of music. (Same for the Beastie Boys and Run DMC.)
So I might be a bit inconsistent in to what extent the song matters when we rate music videos, but I can say the extent it matters is not zero and not 100% either. After all it is a music video list, not a song list, so I am not rating the songs in themselves, but how they work together with a certain visual.