Quick solution for single .(x)html file would be to use Sigil feature "Open With". You have to open two Sigils with books to compare, right click in both of them the section you want to compare and open with something like this script:
Code:
#!/bin/bash
SAVEIFS=$IFS
IFS=$(echo -en "\n\b")
if [ -e "$HOME/.CmpFiles" ]
then
echo -e "${1}\n">>$HOME/.CmpFiles
files=`cat $HOME/.CmpFiles`
xxdiff $files
rm $HOME/.CmpFiles
else
echo -e "${1}\n">$HOME/.CmpFiles
fi
IFS=$SAVEIFS
Instead of xxdiff you could use program of your choice.
This is for Linux of course but must be doable in Windows too.