How to pin a window on top of other windows in OS X? [duplicate]

Try using Helium. It uses a 'customizable translucency' to keep a window on top of other windows. Plus, it won't intercept mouse clicks on top of it unless you want it to.

As of now, it only supports a browser window but the question doesn't indicate if that's a requirement of the OP or not.

I suggest trying kwm https://github.com/koekeishiya/kwm

From my experience, the whole intention of having one window always on top is to read/compare/reference to it while working on another app.

"Tiled window manger" solutions works much better for this purpose. After having tried Athethyst https://github.com/ianyh/Amethyst, I came to kwm. I find kwm offers a better way of configuration. It relies on a config file. After installation, which takes a bit more work then Amethyst, and reading through the sample config file, you already feel yourself a poweruser already. So It's worth to try.

A note though, when I start doing advanced fancy configuration, kwm starts having quite some hiccups.

Edit: kwm is now called yabai https://github.com/koekeishiya/yabai