The Emerald Isles - I never really played The Emerald Isles back in the 2.0 days but when I saw a port for 2.1 I was willing to try it out and I have to say, the level design is pretty great and I always enjoy replaying through the mod from start to finish.
Clock Towers Zone - Introduced a new concept of playing and designing a level with Axis2D. Like Chrome said, nobody other than one other person has used Axis2D for anything and it's a shame. We could really get some cool and interesting level ideas out there using Axis2D.
Glacier Gear Zone - Probably the only ice themed level I can tolerate for a while. Seriously though, this level had some unique ideas with the Wacky Workbench floors and the new goop (at the time) and the music was really good.
Cloud Convoy Zone - Another level made by toaster. I voted this level first place back in the July/August 2014 OLDC and my reason for it still stands. But other than that, it's a really fun short level that takes the concept of Sky Chase Zone from Sonic 2 and adds it to SRB2. I wish this was brought back with an update and maybe see this idea worked in with other themes.