According to Word of God, Effy's first name is Elizabeth. In Tony's S2 episode, the name of the Manic Pixie Dream Girl is Beth, also short for Elizabeth. Then the ending reveals that she was actually a hallucination, a product of his mind
There's also the fact that Janet Montgomery looks more than a little bit like Kaya Scodelario.
The S4 finale reveals that Naomi fell in love with Emily when she first saw her — at the age of 12, three years before the events of S3. And suddenly it's a lot more understandable why she spent the first half of S3 desperately trying to get Emily to admit that she was gay
The show is particularly brilliant with hinting at death. In early S1, Jal reads about loss in psychology class with Chris sitting behind her. In late S2, Chris dies and Jal, his girlfriend at the time, is the one most affected. Shown again when, in Freddie's S3 episode, the class learns about Hamlet and Naomi compares Hamlet to Freddie ("Hamlet's basically a teenage boy. He's got all these desires and he doesn't have the bottom to reach out for them. So, he goes mad, wanks off about Ophelia, and as it's so boring, somebody has to kill him.") In S4, his girlfriend, Effy, goes mad like Ophelia, and Freddie is eventually killed like Hamlet.
The scene where Rob laughs off Emily's coming out makes sense, considering he's married to a woman (Jenna) who does not take the news well and was trying to stave off her reaction (which he didn't succeed at totally). His season 4 interaction with Emily seems to confirm this.
In Nick's Series 5 episode, his dad is played by Dorian Lough, while his rugby coach is played by the much more well-known comedian Alistair Mc Gowan. In a series where parents are typically played by comedians, this seems to show that Coach Pooter is much more of a father to Nick than his actual dad.
Franky's Freak Out in the S5 finale. She runs off, hysterical, and eventually Liv catches up to her. Franky tells her to go away. Sounds relatively harmless — except for the bit where Franky was hanging off the edge of a cliff at the time, raising the possibility that she wanted to die.
There's a worse possibility: Franky only tripped because she looked behind her — had she not, she might have run straight off the edge of the cliff.