Apple - Is there a software that can visually highlight focused windows more?

This is Mavericks specific, but Honer will draw a border around the active window. You might also want to combine it with this app that removes window shadows.

If a paid app is ok, HazeOver darkens everything but the active window slightly. http://hazeover.com

Note that I haven't used it, so I can't speak to it. It has a 4 star review, but the only review for the latest version is negative.

If you're willing to invest some to set it up, Hammerspoon has the hs.window.highlight module that provides:

• Darken the non-active app (like HazeOver)
• Put a border around the active app (like Honer)
• Toggle one window to be isolated (like Isolator)
• Briefly flash a window when it is created

You can further configure this to activate only for some apps. The module is written in lua so I'm guessing you can extend or replace its functionality in the Hammerspoon config file (which is Lua code). For example this config implements a red border around the focused window. There's also a function to turn off window shadows but I haven't gotten it to work.

Having tried Hammerspoon, Honer, and HazeOver, I like Hammerspoon's configurability but I like HazeOver for being well polished, stable, and easy to use. I had tried Honer for a while and liked the way it looked but it wasn't stable on my system. Both Honer and Hammerspoon's border-drawing will lag behind window moves, and sometimes won't catch the window move at all. I haven't tried Isolator.