Is it possible to change opacity of an application window?
Edit: Dec 2018: It seems that a new replacement for Afloat is out called Deskovery,
  You should enter your email here to join the beta program: 
  https://www.neomobili.com/products/deskovery/
  And browse the blog to figure out which beta version you want: https://www.neomobili.com/blog/
  Downloads for all versions of this app are kind of hidden here: https://www.neomobili.com/files/


The previously mentioned Afloat is not working anymore on El Capitan and Sierra since both deprecate applications using code injection techniques.

There seems to be no direct equivalent for this SIMBL using Afloat.

If you now need just a 'mock version', does a mock picture suffice your needs? These needs are a bit underdetermined.

However, you may find a number of possible alternatives available that might offer a somewhat similar functionality:


LayerX
Duplicate-any-windows
Overlay
Overlay2
Uberlayer
GluePrint


These are not tested as to whether they may be combinable.