1) The church battle in chapter ~20 where you fight on one side of the church and then run across to fight on the other. I just love how you have to keep moving around and repositioning and switching weapons and grenades. It really felt like it was the culmination of all that I had learned in the game. I loved that combat environment so hard.
2) Really liked the addition of the Spaniards into the combat. The whole game it sets you up against intelligent and aggressive opponents and then you get to use manual aim most of the time. With the Spaniards, you really can't. You have to run and gun especially in the generator room where they're flooding in. Those creatures put the fear of god in me when I was fighting them and was a really nice change of pace. They started mixing the pirates back in and at the end of the game, it was just pirates. I think they perfectly paced the use of those enemies.
3) The jeep sequence was hella fun. Oh my god, I loved it. Popping a grenade under a truck is probably the single most satisfying half second in the game and you get to do it many times. I was just hoping for trucks to come so I could blow them up.
4) The first two jetski sequences were also really fun. The third one was OK but was kind of oddly paced. When I first started the jetski sequence with the barrels, I didn't know that you could make Elena shoot so I was getting really fucking pissed off because I died about 10 times before I figured that out. I was like "There is no fucking way you can beat this. It's completely fucking random." Then I saw that not only could Ellen shoot but she had infinite grenades for the grenade launcher. I LOVE that weapon. The thing with vehicle sequences is that they really should empower you to just blow some shit up without having to worry so much about dying.
5) Finally, the last sequence on the boat. With Navarro shooting at you, you had to be really careful because you'd get capped if you stuck your neck out long enough. Your cover would also get destroyed so you'd have to continually maneuver around. They force you to use the different weapons in each section and then the last sequence ,which I admittedly died a few times before I figured out exactly what I needed to do, was very cool too. It was like a little puzzle in itself.
6) Quick lighting :O moment. Seeing the foliage shadows sway. Also, there was a small beam of light shining into a corner of a dark room and I just happened to walk over it and I freaked out because I didn't know what it was. Took me awhile to realize the light was shining on my character. Didn't expect that.