There is a Windows binary of htmldoc available, the one I downloaded was at:
http://users.tpg.com.au/naffall/htmldoc.html
The actual website (which contains the documentation and source, but no binaries) is at:
http://www.htmldoc.org/
I've been playing with it for a couple of hours, and the pdf's I've created look excellent on the reader (very readable).
So far I'm using the following settings, I'm grouping the settings as you would see them in the graphical version of HTMLDOC, everything not mentioned I left at the default:
Output Tab
-Output Options: Greyscale
Page Tab
Page Size: 5.24x6.69in
Margins (for Top/Left/Right/Bottom): 1mm
Fonts
Base Font Size: 16.0
Line Spacing: 1.0
Body Typeface: Helvetica
Heading Typeface: Helvetica
Options: Deselected Embed Fonts (this way it will used the fonts built in to the reader)
PDF
PDF Version: 1.4
Page Mode: Document
Page Layout: Single
Options
Browser Width: 800 (I actually used 600 for a bunch of the sites that I've converted but, some sites don't seem to work with anything smaller than 800).
Once you get all of the settings in there (and setup it up to convert a webpage). You can save the config file. It saves in a .book format.
Once I did that, I setup a simple batch file to convert pdf's for a couple of websites that I like to read. Of course you could just use the graphical tool (hit the generate button), but I'm probably going to be converting a bunch of sites every morning, so using the graphical tool would be a bit tedious.
You can use the following command in a batch file:
htmldoc.exe --quiet --batch YourBookNameHere.book -f Whatever.pdf
All in all I'm very impressed at the quality of the resulting PDF's. They look excellent on the Sony Reader.