It's tough to know the demographics of who voted and what they were thinking.
The only reason I wouldn't be surprised that a lot of season 4 episodes were in the top 10 is that they are fresh on people's minds. I watch more season 4 than any other season, but that's because they are still new. I still believe that the 3rd season is the best.
Thus, I think the timing has a lot to do with it. I only saw part of the marathon, and I was very surprised to see "Once Bitten" in the 40's, far above many clearly superior episodes.
It seems like a no-brainer that "Krusty Krab Training Video" should be #1, because that's the general consensus--one even agreed upon by the show's producers, who wrote about it in the Complete 3rd Season DVD box set.