Seeing how the Subtext seems to have exploded in season 3, I've decided I'd better post it in sections cause otherwise it would be way too long a post. My actual thoughts on season 3 as a season will be posted later.
Now onto the subtext between the personable Jennifer "JJ" Jareau working as a media liason and the stoic emotionally remote Field Agent Emily Prentiss. Yes, this truly is an uber.
No.1) Episode 3x01 Doubt
Walking through the Campus they’re working on, JJ and Emily talk about how young everyone is. JJ then says; “All I remember is trying to figure out who I was”. Followed by a nervous little laugh while looking up at Emily. Emily “the strange” then replies with a defeated look on her face; “You move around enough you get used to being whoever people want you to be”. At which JJ looks at her and touches her own lip for some reason (see No.4 for discussion on meaning).
You get a “figuring out”, Freudian orality and a closeted/private Emily all in one little exchange.
[Here we have screencap subtext during the talk about College]
Not to mention the events following. Where a young brunette throws her arms around JJ thanking her for catching the bad guy. All meanwhile Emily looks very uncomfortable and intently keeps her eyes away from the hugging. Feel free to add your own meaning behind her behaviour.
[Even Spencer in the background knows something's going on]
No.2) Episode 3x02 In Birth and Death
Straightforward touching. Emily’s been conked over the head, JJ does the hurt/comfort thing and asks if she’s okay while doing an arm stroke (you know where you start at the other person’s shoulder and stroke down in a reassuring manner). Not much to say, just a simple action that can be overemphasised and pumped full of hidden meaning.
No.3) Episode 3x03 Scared to Death
Standing outside a suspect’s house Emily says; “Why do they always seem so normal?” At which JJ for some unknown reason smirks.
[An oblivious Emily and JJ whose lips are twitching for some reason]
Why would you smirk at a comment like that? Unfortunately there was no time for a witty comeback as the door opened leaving no more room for private conversation.
(enhanced screencaps from Oracle of Quantico)