Wonderquest (Windows, 32-bit)
If you have heard of Deadly Rooms of Death, Wonderquest can be thought of as a DRoD spinoff. It takes the basic idea of the game - you have a sword that stick out one tile in front of you, on your turn you can move or rotate your sword 1/8, and there are roaches, switches, etc to smack with your sword - and throws on top of it something like 10 characters with a plethora of gameplay differences, character switching mid puzzle, a huge dungeon full of puzzles and many elements that aren't seen in DRoD itself.
It is free to download and comes with a level editor/the ability to make and play custom quests.
Falling Hero (third entry on the page) (Windows, 32-bit / Mac OS-X)
Falling Hero feels like if Boulder Dash and Lode Runner were made a turn based puzzle game and grown further. This is a really neat puzzle game, in that all the puzzle elements are presented as having simple, intuitive behaviour, but the quirks of setting it in a side-on environment with instant gravity lead to there being a lot of subtleness to interacting with the environment - you'll have an 'aha' moment so many times over when you realize a new way of moving something around, getting just a tile higher or further, or dodging/manipulating a creature to move in a new way. For example, the Bubble puzzle element - if you push it with your body, it moves one tile. Seems pretty simple, but because you fall down whenever you're in mid air, it seems like you can't move them very far... until you find out that you can push them against sloped/curved surfaces, such as other bubbles, and slide them into new configurations. As I describe, the way puzzles and elements work in the game encourages the player to mess around with everything and make what seems impossible possible through their discoveries.
It has a free to download demo, with ~10 levels spread out across the game's standard level set - not just from the beginning of the game - so you can experience all of the game's difficulty and elements before deciding if you want to buy. And for me, it was an easy choice after the demo stumped me in fun ways :)
With the full game, not only do you get a level editor and the ability to code new puzzle elements into the game (using the game's rather archaic, C-like scripting language - hey, this was decades ago and he wrote it all himself, LUA didn't exist yet, give him a break ;) ), but you can download and play ANY user made level set from the same page I linked above - even ones not made for Falling Hero specifically!
Braid user-made Mods
Do you own Braid for the PC? If you're like me you beat it and wished there was more to do afterwards. Well, you probably aren't even aware that Braid has a not-very-well documented level editor built into it and some brave people have created stunning mods using it. For example:
Silverbraid - the first Braid mod all people should play. A good introduction to advanced concepts that feel like a natural extension of the main game.
Tim's Modyssee - a quirky mix of remixes and originals, hard and simple. A bit of exploration of what pushing the game engine outside of its original comfort zone looks like.
Stone - a remixed version of the original levels, to make solutions much harder.
Nyx - I haven't played this and it only has one world done so far, but I hear it is good.
Nova - the hardest Braid mod of all, from a Chinese modder. Solutions are extremely subtle and rewarding, climaxing in a world 1 that is the full mod in review. Comes with beautiful custom music.
And there are a few more still, check DoctorBalcus's list of braid mod playlists to see.
What about you? Do you have a 'puzzle game no one else has ever heard of, but you wish everyone played'?