Just as the title says.
Examples: Ken Akamatsu's Mahou Sensei Negima
Masquerades as tittilating romantic comedy, and while its inner self is still just a battle manga, it's that kind of concept.

Manga that subvert established tropes in order to improve a story is what I'm getting at.
A manga that ridicules ecchi romance series for their escapism.

Alternatively, manga that forces us to think about things greater than the work itself.

At this point I'm so far up my ass I should stop writing.

Kubera: looks like a typical fantasy/adventure at first. Turns out to be an epic mystery/drama that subverts all common expectations of your typical adventure shounens. Good intentions aren't rewarded. The main character doesn't get her way just because she's the main character (on the contrary), but instead the interactions within the group are continuously developed out over time. All the characters, including antagonists, get continuously fleshed out until they become really multi-faceted characters. What appears to be standard good vs evil turns out to be anything but, instead the races are locked in dynamic imbalance where each side has their own valid points of views.

Qualia the Purple: looks like some cheap yuri at first, turns out to be a mind-blowing dimension-hopping quantum physics saga.

Kokou no Hito: feels shounen-ish at first, but later on is intensely psychological and doesn't give a damn about shounen expectations.