We had some code, tried ApexDoc and didn't like it  since we wrote javadoc and were too lazy  smart to change it.

So... we added some SED and got this cobbled together - This fits out use case, but could def. be refined. What follows is a BASH script that should work if you're running a Mac. 

#! /bin/bash

# Clean the directory up and transfer files. 
# I create a dir called 'doc' in my Eclipse project.
rm *.html
rm *.css
rm -r resources/
rm *.java
cp ../src/classes/*.cls .

# Change the file endings from .cls to .java
for file in *.cls ; do mv $file ${file%.cls}.java ; done

# Pre-Processing the .java files
# 1.) Escape double quotes inside single quotes. 
# Since they are never outside of single quote, just escape 'em
sed -i '' 's/\"/\\\"/g' *.java

# 2.) Remove single quotes and replace with double quotes.
sed -i '' s/\'/\"/g *.java

# 3.) Remove the { get; set; } and replace with a ";"
sed -i '' 's/{ get; set; }/;/g' *.java

# 4.) Remove keywords such as "virtual", "override", "with sharing", etc...
sed -i '' 's/virtual//g' *.java
sed -i '' 's/override//g' *.java
sed -i '' 's/with sharing//g' *.java
sed -i '' 's/testmethod//g' *.java

# 5.) Remove lines with System.assert...
sed -i '' '/System\.assert/d' *.java

# 6.) Remove lines with [SELECT] style queries
sed -i '' '/\[SELECT/d' *.java

# Javadoc it... 
javadoc *.java

# "Post-process" files to remove "java.lang" references. ;) Sshh...
sed -i '' 's/java\.lang\.//g' *.html

# Remove the java.lang.Object inherited methods.
sed -i '' 's/clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait//g' *.html

(That last sed command should be all on one line...)