I'm not sure what the subtext of your comment is, though. If it's "software like this is bad because it enables DRM", that's an odd position to take. If you don't want to obfuscate your code, don't run this transformer on it.
http://www.amazon.com/Surreptitious-Software-Obfuscation-Wat...
For building your own virtual machines, check out the ideas of the people here (Mips virtual machine should be easy, and enough to fool noobie-moderate level crackers) http://stackoverflow.com/questions/573115/what-is-your-favou...
For antidebugging tricks, Peter Ferrie has pretty much written the bible on these when it comes to Windows: http://pferrie.host22.com/papers/antidebug.pdf There's a couple of these papers, make sure you read all of them. For platforms other than Windows, you will have to come up with your own stuff, or Google well :)
For obfuscation, the best tricks are the ones you see in the real world. Check out the excellent Unpackme archives and tutorials of tuts4you: http://tuts4you.com/download.php
Another book on obfsucation that I see get mentioned a lot (which I don't recommend, but it still deserves a mention) is this one: http://www.amazon.com/Surreptitious-Software-Obfuscation-Wat...
And finally, if you're a noobie interested in getting involved in Reverse Engineering, check out Lena's excellent tutorial series: http://tuts4you.com/download.php?view.2876
If you want more info on anything specific, say so...