In person, my favorite homers were:
A home run by Carlton Fisk when I was 11. My dad took me out to Comiskey and Fisk homered in the second game of a three game series. He was my favorite player, so it was a great childhood moment.
I saw Bonds #713th homer, Sunday night ESPN game in Philadelphia, crowd was giving it to him good and he crushed one that went over my head in right field and hit the facing of the third deck, then landed in my row about 15 people to my right. My favorite part was booing Ryan Franklin(who failed a PED test and was suspended) and then asking everyone around me why they weren't booing him too. He actually got a nice round of applause. I don't think anyone got the irony
I was at the HR Derby in Pittsburgh when Ryan Howard hit the 1000 free trips sign to win it all and someone in the stadium actually got free flights for life.
I was at a playoff game in Boston where the White Sox defeated the Red Sox to eliminate them in 2005. Two homers by Ramirez, one by Ortiz and they still lost 5-3. That was the only playoff game I've been to, so all three homers were cool moments.
Without considering everything else, the coolest homer I saw was at a minor league game last year. I go to a lot of games in Lakewood, so I remember a lot of homers there but I never saw anyone hit one over the batter's eye. It's not a hitter's park at all, so there really isn't many homers hit there. Anyway, Cameron Flynn steps up and crushes a line drive to center field that passes the batter's eye and the ball didn't start it's downward ascent until sometime after it got out of sight. The stadium has a walkway around the whole park and there were people a good 440 feet from home plate that watched the ball fly over their head and didn't even bother to chase it because it ended up so far away from them.
Flynn has nine homers in three season of minor league ball. I'm guessing he never hit a ball like that either before or after that homer and I've never seen a ball hit that far before or since.