Kinda similar to the "What's your favorite SRB2 level?" thread, but eh...
Single Player
Egg Rock Zone Act 2: You know the drill, it's like everyone's favorite level. Full of original and very nicely though-out gimmicks. Look at the gravity switcher room for example. It first introduces the gimmick by letting the player do some standard platforming, and then it gets more complicated later on, where you have to do that mid-air jump guarded by Pop-up Turrets. There are few levels that lay their challenges out so perfectly.
Deep Sea Zone Act 1: Definitely wins in the visuals department. Everything is carefully assembled and the sense for detail is incredible. While this level is low on great gimmicks, there are some nice platforming challenges, all of which are seamlessly integrated into the level.
Arid Canyon Zone Act 1: The layout is absolutely amazing; I love how the paths cross each other at several occasions, and the level definitely looks like a canyon. There is a balanced mixture of gimmicks (I especially love those rock spawners, because they are so carefully placed that they pose a dodgable challenge, but a challenge nonetheless) and more traditional platforming that is again perfectly integrated with the theme. The PolyObjects, especially the ones near the end are very clever, and the rope pulley hell at the end provides an unique challenge. The only reason that this is not higher up on my ranking is that the texturing gets a bit monotonous at times.
Egg Rock Zone Act 1: I especially love the right path and its appear/disappear FOFs. The problem here is that the right path is so incredibly much longer than the left one, and also much more interesting.
Deep Sea Zone Act 2: Slightly lower than Act 1, due to some rather uninteresting gimmicks (the bustable block maze, the two waterslide mazes), but still a winner visually and gameplay-wise. The waterslide section on the left path is refreshing, and the Storm-Ruins-ripoff part makes the player gt a bit hectic. I still don't like the waterslide mazes though, mainly because there's always one interesting path and one boring one.
Match (you only get three here, five would be idiotic)
Tidal Palace Zone: The underwater gimmick still fascinates me, as it provides a sudden change of pace. The layout is amazing, it all centers around the usually crowded staircase room, but to gain powerful items, you will need to get off the beaten path. It is very rewarding to snipe a careless victim searching for items or air.
Frost Columns Zone: Though ugly, this one also has a very complex layout that forces you to wander around a bit to get good items. I also love how there is no clear center, apart from outside, you will always find somebody to combat. The slippery ice adds a sense of hecticness, trying to hit somebody while on ice is extremely challenging, and you never can control exactly where you're going.
Thunder Citadel Zone: This one, though complex, has a very easy to memorize layout. The several layers in the outside section are great for sudden sniping attacks, while the lower levels are frequently a rather hectic bomb and grenade fest. The bedroom section gets a bit unused though, mainly because it doesn't have the sought-for Bomb ring panel, which is frequently the only incentive to enter the castle. I also love the Rail ring placement, it's very risky but very rewarding.
CTF (also three, five would be even more stupid)
Nimbus Ruins Zone: Yes, that ever-so-hated death pit fest is my favorite. A very challenging level, where every hit can get you killed and attacks can come from everywhere. Even though I typically lose in this level, I love it.
Lime Forest Zone: For some odd reason, this still plays the best. Due to its small size, it's always rather crowded, and the bases are really brutal. I love the sense of strategy that more or less consists of: Both teams grab the flag, and then the flag runners get hunted down.
Icicle Falls Zone: Rarely played on servers, but if it is, it's quite fascinatingly brutal. The bases are more or less impossible to guard though, and the main reason this is on my top three is that the other CTF levels suck. I do like the multi-layered layout here though.
No Race for you cause I'd be hard-pressed to find enough good levels.