Not all of them but the ones I like and/the ones some missed.
1. Isabel is the same Flight Attendant from Death in the Family
Back in DITF Jason wore a suit on the flight over to see his mother. He sat at the window seat peering out until a blond flight attendant came along and he tried to see if she would give him an alcoholic drink. She suggested a coke with ice instead and he agreed. In RHATO #2 Jason sits at the window seat in a suit staring at his reflection while lost in his thought. Once Roy leaves a blond flight attendant asks him if he's on business or pleasure. Jason responds that there was a death in the family. She gives him a drink saying it's coke with plenty of ice which he comments on her having a good memory. Not to say the characters realized it but it seems impossible for Lobdell to have written these similarities and not be suggesting this.
2. The Brick Jokes-the light and darker versions of it.
A brick joke is basically a callback to something that happened earlier. The lighter version of it happens in #5 when Jason has a flashback to his All Caste days with him completing his tests and awkwardly mumbling a thanks to the crowd that bow to him. Durca mocks his ability to make a speech and Jason points out she trained him to be an assassin not a public speaker. In present day Jason has to flee the towns people after a misunderstanding. When Kori asks why he doesn't try to explain what happened Roy comments that she obviously never heard Jason speak in public.
A darker callback starts in #2 when Roy gets up from his seat while their on a plane and asks if Jason wants anything while he's up. Still trying to push others away and annoyed with Roy pestering him Jason quips that he wants Roy to jump out of the plane wearing a parachute with a hole in it. Issues later in #7 while bragging over the new ship they got from Crux Roy says he's experienced pretty much everything. Including a trip off the Q-Core building without a parachute. Making it sound like he already had one friend toss him away.
3. Jason's Inner Robin Makes an appearance
The same page as the Q-Core parachute mention Jason remarks that if they find Cruxs' lair their likely uncover a "Treasure Trove of Technology." Even Roy can't believe he said that.
4. Roys' Tattoos and Hat
It's easy to see that Roy's right arm has "Poison" written over a scorpion and a skull. The other side isn't so easy to see. From what little we get under Rocafort it appears to have "Pesadilla" written in a scroll above a crown and a two headed bird with a scaly tail. Pesadilla is Spanish for nightmare which added with Poison might be a reminder for him not to give into the temptation of his addictions.
The hat has been part of some surprisingly heated debates since the relaunch. To the point someone claimed it was a worse offense than Lians' death. Others wanted to know what the hell was on Roys' hat. While it started to look like a crown after Lobdell left it's actually a raccoon, it says so on the back of the hat after their return from the Chamber of All. What meaning that has is anyone's guess.
5. Roy Asks about the 300 pound Gorilla in the Room
While in a limo with Kori and Jason in Hong Kong Roy brings up their status as a team. He says that they have nothing else to do except what they were doing. Which brings him to his next topic something he thinks they need to get out of the way and starts to ask about the 300 pound gorilla in the room when they cut him off. There has been some confusion over this and the other two's strong response. They both say in union "one more word and you're a dead man!" Here's my take on it. Roy was saying that they should do what they were doing which was fighting together and well, sex. At least he thinks that's what it was because Roy is under the impression Jason and him both had sex with Kori. He was even worried that was why Jason was distant on the plane ride but Jason told him there's nothing between them. Both told Roy there's no relationship to damage with him sleeping with her. So that issue isn't what he's talking about.
No, the phrase 300 pound gorilla in the room means that he wants to talk about something awkward that everyone's trying to ignore. Simply put: Roy Harper is trying to ask if Jason Todd and Koriand'r want to have a threesome. I'm not saying Lobdell was trying to write Roy as bisexual. In interviews he explained that Roy has no filter between his brain and mouth. In the past not speaking up got him in trouble (again according to interviews not on panel) so Roy feels compelled to clear the air. Because if he thinks their both sleeping with the same woman he has to wonder if the others are thinking about it. This idea is kind of confirmed, at least for me, when Roy grumbles that their too immature to carry an adult conversation. As for their negative reactions, Jason's relationship with Kori isn't actually sexual and I doubt he'd want to hear that suggestion with Roy added into the mix. With Kori, I don't think she'd have a problem with two lovers given her culture but she seems pretty protective of Jason. I think she would have some idea of his comfort zones by then and likely would be irked by Roy going there.
6. The Telltale handprints on Roys' body after sex with Kori
I'm not going to get too detailed with this one but look at them when their in bed together in #1 and #10. The burns her hands leave on the headboard and Roys' body tell just what they did and how.