I thought I'd write a quick advice on using it from what I've learned. The manual dotguide.pdf and the online help are okay, so start there, but keep this in mind :
DOT was designed to make graphs for printing on paper. That leads to some weird quirks. For one thing, all the sizes are in *inches*. It also means that all the fitting support and such is not really what you want, so just disable all of that.
I have the best success when I use the Google method (what I stole from pprof in perftools). Basically they just set the font size and then let DOT make all the decisions about layout and sizing. There's one caveat in that : the way that DOT writes its font size is not supported right by FF3. See : 1 or 2 . There's a pretty easy way to fix this, basically for every font size tag, you need to add a "px" on it. So change "font-size:14.00;" to "font-size:14.00px;" . This change needs to be done on the SVG after dot. I do it by running a grep to replace ",fontcolor=blue" with "px". So in the DOT code I make all my text "blue", it's not actually blue, the grep just changes that to the px I need for my font sizes. So you'll see me output text attributes like "fontsize=24,fontcolor=blue".
The other big thing is that DOT seems to have zero edge label layout code. And in fact the edge layout code is a bit weak in general. It's pretty good at sizing the nodes and positioning the nodes - it has lots of fancy code for that, but then the edge labels are just slapped on, and the text will often be in horrible places. The solution to this is just to use edge labels as little as possible and make them short.
Another trick to getting better edge positioning is to explicitly supply the edge node ports and put them on a record. I do this in my huffman graphs. The other good edge trick is to use edgeweight. It doesn't change the appears of the edge, it changes how the edge is weighted for importance in the layout algorithm, so it becomes straighter and shorter.
For educational purposes I just made a little program to parse MSVC /showIncludes output to DOT :
Here are some Huffman trees (SVG - you need a FireFox 3+ to view nicely) optimized with various Lagrange multipliers :
Remember it's control-wheel to zoom SVG's in FF.