Mac in 'Officer Blue', telling the suspect who shot the mounted officer that he'd execute him with no trial. Not to mention Stella in that ep. Fanservice yes, but still awesome when she plants the rifle on Mac's desk.
The end of 'Indelible', besides being pure tearjerker
Lindsay getting her medal after rescuing Danny and Lucy from Shane Casey.
Mac and Flack using the situation to their advantage to rescue the baby out from under the (deaf) kidnapper's nose in "Silent Night".
Mac, Stella and Sheldon defending the Crime Lab from the drug smugglers in the Season 3 finale "Snow Day".
In "Damned if You Do" Jo is interrogating a young man accused of beating his father to death and his mother to near-death. He claims that he was at a frat party but doesn't have an alibi for the timeframe in which his parents were attacked. Jo proceeds to calculate down to the minute how much time it would have taken him to leave the party, attack his parents, change and return to the party without anyone else there being the wiser.
Suspect: What are you doing?
Jo: Math. Because you're not man enough to admit what you did, now I've gotta do math. I hate math.