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Random bunch of things that most of you will probably know, but perhaps someone didn’t know:
1) When Smith overtakes someone by making them all silver, this is a direct reference back to when Neo put his hand into the melting mirror. The melting mirror was showing that the world is breaking down, and the mirror between the Matrix and what is behind is begin to show. In M1, it connected back to his point of origin, the pod, where his true self resides. Now if Smith tries to overtake an agent, he will travel right back to where the programming for that agent exists and copy over that. When Smith overtook the Oracle, he travelled back to her main code and thought he had copied over it, and because she is one of the creators, Smith FINALLY has the power to break the matrix (Agents can only bend the rules, so they cant fly, people like Neo can though which is why once the Super-Smith is created, he is the only one who can match Neo and can break the Matrix too, enabling him to fly etc.
2) When Neo and Smith are fighting at the end, Smith is oblivious to the fact that Neo is sitting right in the middle of the machine city. He tries to overtake Neo just as he tried before, but instead of travelling to where Neo is sitting inside a ship and copying over him, Neo is plugged right into the grand daddy of the Machines, and travels right back to the source, which is where Smith really does not want to travel too. Now that there is a direct link from Smith to the Dues Ex Machina, you see a huge jolt run through Neo, and instead of Smith overwriting the Dues Ex Machina (good luck!), he taps right into Smith and deletes him.
3) When Persephone wanted Neo to kiss her and prove he was in love with Trinity, she wanted to make sure that if she helped Neo get to the source that he would refuse to kill Trinity and crash the entire matrix (something Merv was trying to stop, hence his stealing of the keymaker, although he was probably just expecting a reboot as before not an entire system crash), hopefully deleting the Merv and herself. I think that because all the previous ones have made the right choice, Merv has always been able to survive possibly by hiding out in Mobile Av while the system reboots, but Persephone is sick of him and has had enough and wants an entire system crash (as the Architect threatens). So to make sure that if she sends Neo to the Architect , and he presents him with a choice, she wanted to make sure that he would choose to save trinity (she knows, as Merv knows, that in the past previous ones only had a general love for the human species and chose the correct door, where as Neo was different, and if he truly was in love, which she tested with a kiss, Neo would tell the Architect to go and get boned instead)
4) When Neo is in the interrogation room in M1, it shows the camera travelling through the architects room of monitors. Ok, obvious but hey someone might have missed it!
5) A common suggestion is ‘why didn’t the machines just use solar panels above the clouds?”. The answer being that as shown in M3, anything that goes near the clouds has all energy destroyed. So while they might be able to erect thousands of stupidly tall solar towers, the clouds are just going to destroy any power running through them anyway. I hear that question a lot 
I just watched the movies again last night and those were a few little things I picked up on 
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