Before anyone gets intimidated by this trophy, just know that this trophy's image is deceiving.
There are a total of 278 challenges in this game. To unlock this trophy you need to get 100 of the 278 (hardly 100%
Challenges are pretty basic, with some trials thrown in the mix. Most challenges are relatively easy (Chameleon, Infiltrator, Suit Only, etc). Sometimes you have to kill certain people in certain ways, sometimes you have to interact with your environment in certain ways, and sometimes you need to just do something without being seen.
I got my 100th challenge done right before Skurky's Law.
Also, please note that challenges can not be completed on Easy - you need to be on Normal difficulty or higher.
Lastly, if you complete a mission, and missed a few challenges, you can go back in unlock more at any point.
Questions, corrections and Neg Vote Justifications below.