1) The first time McGee kissed Gibbs it was an accident. The Norfolk office was so cramped and cluttered that McGee tripped and their lips collided. He was blushing so red after that and couldn't look at Gibbs for the rest of the case.
2) The second time Gibbs and Tim kissed was when Gibbs was nearly blown to death by Pin Pin Pula. Gibbs had been to his house, packing up the few things he was going to take to Mexico. He was drinking a bit too much that night when Tim came over to check on his boss. Gibbs was slurring his speech and regretting many things, not even noticing when McGee came in. He yelled at McGee saying how sorry he was for being a shit boss and leaving his team. McGee hugged Gibbs, trying to comfort him when a drunken Gibbs kissed him. McGee just lead his boss up to the couch and made sure he fell asleep before he left. They didn't see each other for months after that.
3) The third time they kissed, they were in Los Angeles, visiting the Office of Special Projects. Tim had gotten himself into a predicament at the hotel bar and he visibly looked uncomfortable. The man was clearly drunk and harassing Tim so Gibbs decided to step in. He wrapped his arms around McGee's waist and kissed McGee softly but passionately. The man left McGee alone after that and McGee just flushed red at his boss. That was the night Gibbs found out McGee was a cuddler when there was only one bed in the hotel room.
4) The fourth time they kissed, McGee thought he was going to die. His green eyes were wide with fear as he looked down and saw the shard of glass impaling his side. Gibbs had cupped his cheek and kissed him softly, whispering to McGee it would be alright. McGee almost collapsed at that moment, but didn't want to seem weak, so he kept up his strength. The team leader sat down slowly and pulled McGee into his lap, stroking his hair gently until the EMTs could get him to the hospital.
5) The last time they kissed was right before Gibbs got shot by Luke Harris and after Dorneget died. Yes, Gibbs knew McGee was dating Delilah and yes, Tim was aware of it himself but he always found comfort with Gibbs. Gibbs stopped the elevator as usual. McGee was about to burst into tears when Gibbs placed a soft kiss to his lips. McGee accepted the kiss and then burrowed his head into Gibbs' shoulder, crying for what seemed like hours. Gibbs silently comforted McGee, making sure he was alright and he had everything he needed. The younger agent sighed and Gibbs told him to go home and spend time with Delilah and his dog. Gibbs watched as the younger man went, knowing the same feelings of regret from years ago.