An understated one, but way back in Season 2, Don is being targeted by the Russian mob, and it's made clear they will go after those closest to him as well. Two men show up at Charlie's lecture, and he manages to send them away without inciting panic. That he is clearly under tremendous strain just shows how awesome he is for keeping his head.
In the Season 6 premiere, Charlie manages to figure out the exact position of a sniper using math, while being fired on.
A far cry from his situation five seasons earlier in "Sniper Zero".
In the Season 5 finale:
Amita: My book will be called "My 3 days with a computer illiterate!"
Charlie weaponizing an MRI machine on an assassin in "Janus List".
Charlie talking to the man that stabbed Don:
Killer: Is it worth your life?
Charlie: It's worth this moment. Meeting the man who stabbed my brother.
Killer: Your brother? The FBI agent?
Charlie: *drops the millions of dollars of diamonds the man had been looking for as the agents swarm in*