There have been a huge list already but I don't remember if 'Body of Lies' has been mentioned already. Anyway it's my vote as well as modern Bonds (Craig era) and Bourne movies.
I am not sure if this qualifies (or is this more PI stuff) but which at least gave a good tone was TV series 'Equalizer'.
I think the Equalizer is a little like Burn Notice with its "ex ops dude helping out regular folks altruistically" premise.
There's a '70s British TV show called Callan with Edward Woodward, actually. I haven't had a chance to see it yet, but I've heard its a good darkish spy/assassin show. I also heard that the character he played years later in the Equalizer could be based on that role.
Equaliser was Callan gone Freelance.