(x-posted because the same long and rambly answer covers questions in two threads)

I don't often write with a theme in mind, but my stories do generally wind up with a unifying message by the end. I very much believe that stories, any stories and all stories, express something about how the author views reality and what the author's values are. When it's done poorly or done too strongly it comes off as anvilicious/ author filibuster. When it's done well it's subtle and the reader might not even notice (Especially if it meshes with the reader's view of reality is in tune with the author's)

Interesting trend I've noticed in my own work: My YA-aimed fiction tends to be a little more clear-cut/heavy on its message than my adult (erotic, mostly) fiction. This is because my erotic fiction has about as much substance as whipped cream, whereas my YA fiction is meant to probe questions about society and humanity and such. Examples; my two current projects:

Book 1: Steampunk-Fantasy erotica. It's AU 1868, the US civil war has just ended via the Union dropping Radium-Cobalt bombs (effectively nukes) on the southeastern US, US colonization happened differently anyhow so the maps are all drawn differently. Characters A and B are brother and sister, are rich, and are black. In Boston. In AU 1868. Character C is a recently immigrated Irish werewolf whose family are high-ranking figures in the Irish mob. Character D is a polyglot hired as a translator for character C. A and C and B and D have sex. Lots. Conflict comes from social polemic concerning race (real racism and fantastic racism), class, immigrant status, and sociological ramifications of the associated relationships as pertaining to Victorian social mores. Mostly a romp.

Book 2: Soft Sci-fi YA fiction. Several generations post human colonization of a distant earth-like world via generational star ship, a group of 24 children ranging in age from 4-16 find themselves stranded in an outlying pioneer town with no living adults (I promise there is a non-a** pull explanation for how this occurred having to do with indigenous culture and who it's acceptable to mercilessly slay...) and no feasible way to contact the larger colonial civilization. At the time the book begins they've been holding out for two years, largely trying to stick it out until a rendezvous party just happens to find them. Their capacity to survive largely hitches on the aid of a young woman who through plot machinations was raised by indigenous aliens. The book explores the ramifications of colonialism, the nature of personhood and human identity (for TVtropers, what measure is a nonhuman), the nature of gender (the indigenous aliens in question do not have gender - they are biologically hermaphrodites that reproduce by spawning), family and kinship networks (the aliens do not arrange themselves into nuclear families), the development of cultures, cultural enmeshment and fusion, coming of age/adulthood and its definitors, and what constitutes community. The book culminates when the kids are able to re-initiate contact with the larger human culture, but they choose not to be 'rescued' and reintegrated into the larger culture, having over the course of the novel become their own distinct and unique cultural unit (noteworthy: The oldest members of the group are in their early 20's when this happens, and some have coupled and had kids of their own). They've also made successful cultural contact with the indigenous people in ways that no other human society has, with the implication that this will result in cultural revolution throughout the larger human and indigenous cultures.