I've published some children's fiction this year, but I suspect I will publish programming works again at some point.
I'll give another plug for Scrivener, which is really a great tool. All of the editions that I have in the major online bookstores come straight out of Scrivener (though I obviously used an image editor for the covers).
I wanted to also mention out awesome Leanpub is. Write your files in Markdown (and they support code snippets well... definitely a service that works well for software topics), save them in Dropbox. Press a couple of buttons in your browser and you've got PDF, mobi and epub. And, you can sell right away and keep 90% - 50 cents. They make it easy to publish early in the process and keep readers up to date as you complete the work.
One bonus that's not as obvious: Leanpub also makes distribution to a sample audience easy. You can generate coupon codes trivially.
I'm planning to go straight to Leanpub with my next technical work.
The only complaint I've heard about Leanpub is that they don't give the author access to end user email addresses. I don't use email as a marketing tool much (almost never) but I would guess this could be a show-stopper for many eBook authors who are considering their solution.