ePubPack[1] to create the ePub, FlightCrew[2] to validate the ePub, Calibre and iBooks on the iPad to preview. For Kindle books, I use Mobipocket creator[3]. Kindlegen[4], the tool Amazon provides to convert ePub to Mobi didn't output consistent results so I stopped using it.

I'm by no means an expert, so there may be a better set of tools out there but these have worked well for me.

[1] http://sourceforge.net/projects/epubpack/

[2] http://code.google.com/p/flightcrew/

[3] http://www.mobipocket.com/en/downloadsoft/productdetailscrea...

[4] http://www.amazon.com/gp/feature.html?ie=UTF8&docId=1000...

TeX and LaTeX. Still the best software available to translate structured markup to a pdf.

If you are doing anything with equations, LaTeX is definitely the way to go. Unfortunately, it's a steep learning curve for regular ebooks.

The downside is it's not super HTML-friendly (there are converters, but you can't display equations easily in HTML) so converting to Mobi, ePub, etc. is not straightforward.

Certainly it has a steep learning curve but it has a very large community that supports its packages and now also has a friendly and helpful community http://tex.stackexchange.com/

They can be as friendly and helpful as you want, but that doesn't change the fact that the input format for mobi and epub is basically HTML; meaning that by utilizing TeX, you are basically adding another layer that doesn't provide much value. The beautiful fonts, formatting, spacing, etc.. etc... that TeX provides will all be lost on your ereader.

I unfortunately do not have much to add by way of recommendations for software to use. However, one extreme painpoint for me as a consumer of eBooks is PDF. PDF documents are bad enough when trying to read them on a full computer monitor; on a Kindle or a Nook they are nearly unreadable, and on smartphones they are a complete non-starter (for me, at least). I would strongly encourage you to focus on formats that can be dynamically be resized based on the viewing area (e.g. ePub or Mobipocket) rather than PDF.

I have material I self publish using Drumlin Reader due to the extremely low cost and inclusion of DRM. Due to the nature of the particular market, Windows only is not a significant drawback.

http://www.drumlinsecurity.com/

LiberWriter, of course: http://www.liberwriter.com

Lazy option: Print to PDF. I've only ever done it from web pages so far, it's good if don't want html (there was a good reason at the time, forgotten).

The easiest way is to create a document in Google Docs and export it as a PDF