>>I use enigma. I bought paid version but unfortunately paid version protects .EXE file also after packed it. Protected version runs slow with atom cpu POS computers. So I use free version... :(
I think this is excellent advice if you're wanting to supply a single file with all dependencies: the free Enigma Virtual Box does a good job of this.
However, if the goal is to protect then unfortunately the free version is moderately easy to unpack.
The paid version also can be unpacked (using OlyDbg if necessary) but as you note, it messes with the exe so it doesn't work outside the repository.
For others: worth noting that digital signing should be conducted AFTER any form of packing, or the signature will be invalid.
Finally, any sort of protection/compression creates risk of virus signature that can cause quarantine or alerts because some viruses use similar techniques to shield themselves. This is extremely annoying and also affects other products.
"... They ne'er cared for us
yet: suffer us to famish, and their store-houses
crammed with grain; make edicts for usury, to
support usurers; repeal daily any wholesome act
established against the rich, and provide more
piercing statutes daily, to chain up and restrain
the poor. If the wars eat us not up, they will; and
there's all the love they bear us."
-- Shakespeare: Coriolanus, Act 1, scene 1