I've noticed so many subtle parallels and similarities, as well! Like how Jemma tells Daisy: "I can't lose you too!" When Daisy wanted to fight the androids and help her and Jemma escape. And Clarke also tells Bellamy those same exact words: "I can't lose you too." When talking about sending a man into Mount Weather in order to help their people.. escape!
Then you have Octavia kissing Ilian and telling him: "just make me feel something else." Right after she tried to kill herself. Similarly to how human Aida (or Ophelia) was upset over Fitz rejecting her, so she says: "make me feel something else" to Ivanov (who ironically enough also plays Roan in The 100) and then starts making out with him.
Also in Mount Weather when Octavia was yelling at Clarke for trusting Lexa and Clarke yells: "I am doing the best I can!" And Octavia responds: "well it isn't good enough." Something similar happens with Daisy and Yo-Yo when Daisy tells her she failed to bring Mack back from the framework. Daisy yells: "I tried! He didn't want to come back!" To which Yo-Yo responds: "who cares!?"
Yet another parallel is when the 100 first landed on Earth (technically a new planet to them) and Octavia went for a swim and got attacked by that creature. When Jemma was teleported to another planet (a new planet to her) and she found water, she went for a swim and was attacked by a creature.
To add on to Jemma being on that planet, she recorded a video of herself talking to Fitz, and I'll quote some of it: "Been on this stupid planet for a month now. I don't know why I'm still talking to you – why I'm recording myself – you're never gonna see this, are you? I really need you to come and get me, okay? I know you won't give up, so I won't either." And later in the episode she sees Fitz's flare. This is extremely similar to the finale of season 4 of The 100, when we're shown what happens six years later. Clarke pulls out her walkie-talkie/radio and begins talking to Bellamy: "It's been 2,199 days since Praimfaya. I don't know why I still do this everyday. It's been safe for you to come down for over a year now. Anyway, I still have hope." And after a few moments, she sees an aircraft coming out of the sky.
And like people have been talking about, the storyline of Aida and Alie are so similar. Both were AI's/robots who created a "perfect" world and attempted to take away people's pain.
There's dozens of smaller parallels I'm forgetting, but I just remember watching AOS and being like "omg, another reference to the 100?" Their similarities are uncanny.