Kongregate version?

[Keybounce]

So there's a version of the Creeper worlds on Kongregate.

How does it differ from the commercial version?

For CW1, I found the tutorial missions, a set of user-made levels, and a "new map every day" version.

Is the gameplay identical, and the only difference being the maps in the full version?

[GoodMorning]

CW1, yes; it also gives you access to many more handmade (read: more interesting) maps.
CW2, the web version only has a handful of maps, the web version is essentially a demo.
CW3, same as CW2 (plus browser changes since the web-CW3 version was made mean that the web one is slightly unstable, now).
Particle Fleet doesn't have a web version, nor is CW4 likely to.

Having played each, but CW3 specifically, I can say that the paid version is easily worth it if you enjoyed the web version. Especially since people have scripted things to let you play as the Creeper, or against a Creeper version of your own units, or play as anti-creeper.

TL, DR: The web versions are demos, the CW1 map generator is OK if you like it.