Nice work! Here are a few comments from my first playthrough:

1) Since the controls are a little nonstandard, it would be helpful to have bigger, more obvious help about them. That is, when I see [UP/DOWN] aim, [x] fire, my eyes glaze over because it looks like code. Instead of text, try using pictures that look like keyboard keys with arrows nearby.

2) Consider putting movement on arrow keys (up, left right), and putting aiming and shooting on a different set of keys (z and c for aim, x for shoot; or z/x for aim, space for shoot). The reason is that just about every flash game in the world uses arrows for movement.

3) I'd strongly recommend making your character's arm/gun thingy much more prominent and obvious. I've been playing your builds ever since you finished space squid and I didn't notice the aimer until now. I seriously had no idea you could even aim.

4) On level 3 or so, you are introduced to Hydrogen. It's a neat level, but there should be a ramp or something to let you get back up to the hydrogen if you fall to the bottom level. At the moment it's possible to get stuck down there with no way to win, which is no good in a tutorial level. Or any level, really.

5) I think it would be better to introduce the three types of bonds in three different levels.

6) I have a tough time telling the difference between the explody atoms and the ones I'm supposed to grab. The colors are too similar. The explody ones should have a different shape or some danger lines or something.

7) I also can't remember the mapping of element name (oxygen, etc) to visual representation (greenish circle, etc). Could there be a bit of text that pops up when you hit them (Oxygen collected!) to help me learn it?

8) Shouldn't the bonds poof away when one of the atoms on either side is destroyed? The current behavior doesn't make sense.

9) "Aluminum" isn't what I think of when I think "super heavy thing that can kill me". How about Iron or Lead instead?

10) The "hold down z to wall jump" hint was great. I'd recommend making it even more prominent, like the "build to the pipe" sign on level 1 of World of Goo.

11) The help text about "falling off screen is deadly" was confusing to me. The point of this level is to teach the user that he can drop nitrogen off-screen to destroy it. But why are we destroying nitrogen, when we can leave aluminum behind? How about just make it so you don't have to destroy nitrogen to win a level? And then protonaut's mission becomes much, MUCH easier to explain: collect gases.

12) I'm only just now noticing the help text below the game screen. I think most people ignore stuff outside the game screen because it usually useless stuff like ads.

13) Final Exam: Ack, it's possible to miss a ball a the top and then be stuck at the bottom with no way to finish! Also, there are a few "leaps of faith", where you have to jump into the unknown.

14) Can jump be made to work continuously when held down? It's great when you are wall jumping, but it should also work that way when walking.

I hope this is helpful. IM me sometime; I've got plenty more to talk about.

Rob