Hannibal can read people really well.
As another poster mentioned, he knew Will's love of killing people, manipulated him into a situation where he would kill, got Will to confess, then immediately made himself a non judgemental ear. Not only that, he took advantage of Will's empathy disorder and lack of social graces. In the very first episode, he enters Will's hotel room while Will is still in his boxers, which is very non professional behaviour. And Will copies this behaviour - three episodes later he's turning up at Hannibal's house while Hannibal is in sleepwear. Which is what Hannibal wants - for their relationship to be personal as possible. He also keeps stressing on Will's obligation to Abigail and how they're her fathers, when the thought didn't even enter Will's mind before Hannibal put it there.
From a few meetings with Beverly he got a sense of her personality - her strong sense of justice, her willingness to forgo the rules, and manipulated her accordingly. He left clues on the muralist which made Will's accusations seem credible, which led Beverly to break into his house to recover evidence, where he lay in wait. Hannibal even played on her guilt manipulate her, saying that it was Beverly's knack for finding evidence which put Will behind bars (framed as a compliment at the time of course). If Beverly never inspected the fishing lures, Will might not have been tried as the Copy Cat.
Apart from that, Hannibal tends to tell people that they're right, their feelings are valid, and is an easygoing person, which makes people trust him and have a positive association with him. He also gets people to collude over small secrets - Will's psych eval, Bella's cancer (he made that comment about smelling cancer in his youth because he knew Bella would catch on and come to him), Jack's guilt about Miriam Lass, the whole thing with Donald Sutcliffe, acting as co-conspirator to Chilton's psychic driving...etc. Secrets have power, the more secrets Hannibal amasses, the more control he has over the narrative. If he's unable to sniff out a person's secret, he'll create a secret for the person with which he can control them (eg, getting Abigail to kill Nicholas Boyle and hide his body).