Any really good puzzle games?

Lilly Looking through
The Silent Age.

Samorost from the same dev seems ok, but short.

I highly recommend Qbeh-1: The Atlas Cube
Though it might be a different style than what you're asking for.
I liked it better than Portal.
Please don't hurt me.

I suggest trying out World of Goo. Not as simple as a point & click but still really easy to pick up.

Lumino City.
I really like the art design. :)

I can't say, as I have never played Machinarium, but graphically, the Deponia series looks alot like Machinarium. I have just started playing the first, so can't say how well the puzzles are in the game. http://store.steampowered.com/app/214340

I also recently finished off Frankenstein: Master of Death http://store.steampowered.com/app/347430 and Dracula's Legacy http://store.steampowered.com/app/396790, which were fairly good Puzzle games with some find the hidden item games in it as well.

Spacechem and Hexcells!
Neither are really very Machinariumesque... But they are the best puzzle games ever made.
You're not really playing a puzzle game until your brain starts hurting.
That stabbing pain above your left eye is how you know you're having fun.

Although I haven't played it yet, Unmechanical reminds me a bit of Machinarium in that it's puzzles with robots. Violett Remastered is more of the 2D puzzling like Machinarium, and somebody above mentioned Samorost 2 made by the same devs.

Oh-- and The Tiny Bang Story was also Machinarium-esque. It's also currently 60% off on Steam.

idk if its counted as puzzle but I do recommend the game the treasures of montezuma

did you play braid? it's not similar to machinarium but it's also awesome.

there's also winterbottom if you like puzzles.

I play a lot of puzzle games, but not usually point and click so our tastes may be a bit different. My favorites are:
SpaceChem
Braid
Portal (1and 2)
Antichamber
Limbo

For Android I like Trainyard, and LYNE isn't bad.

Bik is a nice adventure game with a cute story, more comedic, varied puzzles and fun achievements. It doesn't have the luscious artwork of Machinarium, though. It's on Android, too.

I also adored Botanicula from the Machinarium devs. It has a different style of puzzling, with collectibles, but much better than Samorost imo.