Charles Stross packs more ideas into a chapter than some authors put in an entire novel. His book Accelerando, a multi-award winning collection of related short stories, was chock full of page-to-page Hard SF Big Ideas. Glasshouse, a more integrated novel, does almost the same thing but with Soft SF themes. After all, when you trip across a minor character named "Alice Sheldon," you know that you should be on the lookout for gender issues. But since this is Charles Stross we're talking about, that won't be the only theme he hits by a long shot.
The foundation of Glasshouse is a basic far-future "uncover the evil scheme and defeat the bad guys" plot. It's all told from the first person perspective of Robin, an ex-military man recovering from extensive memory surgery. He believes that there are still those out there who wish him harm, memories or no, so he agrees to follow Kay, a fellow patient and love interest, into an isolated sociological experiment. There's a great scene where Robin's artificial psychologist is encouraging him to join the experiment, clearly evoking the computer psychologist who attended to Robinette Broadhead in Frederick Pohl's Gateway.
The experiment is being conducted, ostensibly, to try to recreate the sociology of the deep, dark past, a time mostly forgotten due to repeated censorship wars, memory viruses, and the degradation of digital media from the time in question: 1950-2050. So they take our very post-human, very Heinleinian hero, and reincarnate him as a small woman named Reeve. Everyone in the habitat has a new name and identity, and all are being forced to live within the limits of "normal" (to us) human bodies.
To try and recreate ancient society, there are rules and a point system for enforcing the rules. When you act "in character", you are rewarded, and likewise punished for acting anachronistically. At the end of the experiment, there will be large monetary bonuses for high scorers. When all the groups meet up at church for the week, they can also punish each other for perceived infractions of the social order, under the encouragement and supervision of one of the experimenters, acting as a priest. (See, I told you it wouldn't just be gender themes.) Obviously, the people running the experiment are not acting as disinterested observers.
The social set-up of the experiment harkens back to that of the Western 1950s. As such, it is a bit of a strawman. Obviously, things have changed a lot for women since then. On the other hand, it is a very realistic choice. Considering how much information from the 1980s forward will be kept on digital media that will be impossible to read in the future, it is quite possible that future historians will know much more about the 1950s than the 1990s. Plus, it does allow Stross to deal with several themes on a more detailed level. In the church setting, public acts of nonconformity are held up to the community and ridiculed or punished, reinforcing group solidarity. However, the privacy of the nuclear family is still basically respected, allowing horrible acts of domestic violence to go unchecked.
Here's where we start to run into a little trouble in interpreting the story. There are only two fully fleshed out characters with emotional depth: Robin/Reeve and her "husband," Sam (note the use of gender-neutral names). Both of them are deeply damaged by their wartime experiences, and both are severely uncomfortable with the bodies they've been given. Thus, they continually stand out as the other characters take to the scoring system with a vengeance, especially the other "women". Interestingly enough, Robin/Reeve (essentially male) wants to stop the aforementioned domestic abuse as it is getting started, but is prevented by Sam (essentially female) who is nervous about rocking the boat or calling attention to themselves, thus allowing the abuse to progress. If society on the outside is as loose and tolerant as Stross suggests (where you can wear any type of body you want, group marriages of various iterations are common, and bodily injury is never permanent), why would the other characters adopt the strictures of the experiment with such glee? Would the monetary incentive at the end really make people OK with lynching (in a situation with no instant body repair)? Possibly Stross is suggesting that the experimenters have been messing with people's minds to a greater extent than is stated explicitly; he does mention that Robin feels like he may somehow be immune to propagandizing. Another example is when Robin discovers that it is possible to get actually pregnant in this habitat; it is so shocking to him that he literally throws up. On the outside, no one ever has to give birth naturally anymore; it's too dangerous. Yet, the other women seem only mildly put out by the prospect and some think it's great because of the additional score bonus. In the end, without being able to get into the heads of any of the background characters, it seems like our heroes are unjustly privileged over the rest of the cast.
In the post-human future that Stross describes, gender identity has been completely separated from your physical body. After all, you can change your body almost at will. When we first meet Kay, she's wearing a body with four arms and blue skin, looking basically like Kali. Before that, she had spent about 50 years being an alien—doing sociological research from inside an alien society, even joining in a family unit. When Robin was in the military he was literally a tank: he weighed two tons, was three meters tall, didn't need to eat or breathe since he was fully self-contained and nuclear-powered, and sometimes he commanded a unit of his own selves—up to a hundred of himself. To think that someone flexible enough to still have a clear sense of self after all that would be so discombobulated at being in a "normal" woman's body is a little off-putting, but it's perhaps understandable in that he's never had to accept limits on physical strength and recuperation before. Robin is described as being abnormally wedded to a male-type body, and Sam, having spent time as a male in the past, has very negative associations with being that gender. So while gender is a much more fluid concept in this far future, it is still an important concept and these characters still self-identify strongly with one gender or the other. It seems that while gender identity may have been liberated from the static state of the body, it is still strongly linked to personality types. Robin is a very military man, even when he is a she. He's a natural leader. Sam, on the other hand, is much more passive, fearful and nurturing.
Another strong theme in Glasshouse is the fluidity of identity. When your memories and everything that make up the entity you think of as "you" can be backed up and stored and even hacked, how do you know when you've changed? Or at least, when you've changed when you shouldn't? After all, we all change given time. We're not at all similar to the people we were when we were children. So you can't preserve your personality by being static; that would be useless. On the other hand, it is then hard to identify when changes have come from the outside, as opposed to happening naturally. Stross gives a particularly chilling illustration of this when he shows the results of Reeve being brainwashed, without her knowing it, and continuing to describe her own perspective in the first person narration. It's a brilliant job of writing, just subtle enough to be creepy and effective. The most important message that Stross appears to be conveying is: "Fight Conformity!" Those characters that jump into the game of winning and losing social points are the creepiest people in the whole story, and they would be the enablers that allowed the horrible designs of the experimenters to come to fruition. It is only a small group that has the will to fight the system, led by Robin, that stops their plot. This probably constitutes preaching to the choir, considering the self-image of your average SF fan, but as moral tales go, this is an enjoyable one.
In the end, Robin is able to find allies and a way to thwart the designs of the experimenters. When the ending comes, it is surprisingly abrupt and the denouement can only be described as odd. However, the story up to that point has been easily fascinating enough to make up for it. Along the way, we are treated to a host of SF references, homages to some of Stross' influences. The tank unit that Robin had been a member of was the Linebarger Cats, for instance, and a nice character named Mr. Harshaw is a nod to Robert Heinlein, obviously a huge influence on Robin's hyper-competent military character. As with all of Stross' work, the action moves fast and is well-thought-out, and there's a good sense of humor about the whole thing. Even when wrestling with these complex issues of gender and identity, the whole thing remains an adventure at heart, a downright fun story.