All Fall Down: Bad things happen. You deal with them, because they're not just going to fix themselves.
Astro City: The ordinariness of the extraordinary.
Avengers Academy: Choosing to do the right thing, even if other options are easier.
Also, acknowledging and learning from past tragedies without letting them define you.
The three different series of Batgirl each have three different overarching themes:
The 2000-2006 series featuring Cassandra Cain is about innocence and redemption; specifically, about how innocence can be corrupted and what is required to redeem someone for the wrongs they've done in the past.
The 2009-2011 series featuring Stephanie Brown is about heroism, and what it takes to be a hero even if no one else thinks you're capable of it.
The post New 52 series (2011-present) featuring Barbara Gordon is about healing the wounds of the past, whether physical, emotional or psychological.
Batman: How the traumas of the past affect the choices we make, and thus how they shape us into the people we are in the present.
In particular, practically every member of Batman's Rogue's Gallery either reflects a part of Batman himself and/or like him has an over-arching trauma that has shaped their lives ever since — except where he has used his trauma to make himself a better man by defending the innocent to try and prevent what happened to him from happening to others, they have succumbed to despair and evil and use their traumas as an excuse to hurt others.
The Boys: The pathetic inadequacies of superheroes and the futility of relying on them (both in-universe and, in a meta-sense, as wish-fulfillment figures) to solve the problems of a complex world.
Alternatively, horrible ways in which corporate greed destroys everything by applying half-baked, poorly put together, but easily marketable and profitable solutions to complex problems and using corruption to make them first choice options instead of something that would actually work.
Also the sheer bizarre wonderfulness of the universe and the dangers — and opportunities — that exploring it can hold.
Flex Mentallo: Don't throw away things you love because they are seen as immature, silly or stupid.
From Hell: The fundamental interconnections that exist between everything and everyone, and how a serial killer is both a product of society and culture as a whole and something which goes on to shape that society further.
The work of Geoff Johns frequently revolves around themes such as family, managing your emotions and finding your place in the world, with the theme corresponding to the overall motif or theme of the character(s) he's writing for. For example:
His Green Lantern run spanning pre- and post-New52 revolves around overcoming fear and accepting your emotions.
His The Flash run explores the character's need to 'slow down' (i.e. take time out every now and again).
His Aquaman run looks at what it is to be an outsider
Global Frequency: The extraordinary things that ordinary people can do if given the chance and resources to do them. Also, how no skill or ability is truly worthless, and how even the most seemingly trivial or obscure forms of knowledge can, if applied in the correct setting, do amazing things.
Judge Dredd: The law, no matter how harsh, really is there for your protection.
Alternatively, the extremes that unthinking, unyielding and over-oppressive fascist law-enforcement can go to... and the kind of society that would need this kind of law-enforcement in order to function.
The Wicked And The Divine: Accodring to Word Of God, the relationship between art and its creator, how choices and compromises artists make influence their creations, their audience and their very lives.
Wonder Woman: The conflict between the desire for peace and how it may be sometimes necessary to fight in order to ensure it.
X-Men - Choosing to do the right thing, even when faced with prejudice and injustice. More specifically, having to choose between using your abilities to help mankind and using them to rebel against an oppressive establishment.