This is basically a roadmap on what you should be doing in order to get all of the trophies/achievements in Dishonored. Since it will take at least two playthroughs of the game to do everything, you should concentrate on those two playthroughs. Note that there's no difficulty trophy/achievement in the game, so you could do everything on the easiest difficult setting.
Low Chaos Playthrough
Low Chaos basically entails you not doing a lot of killing, so this should be your stealth playthrough. Since that is what it is, you will want to concentrate on getting Clean Hands and Shadow , which are to not kill anyone and not alert anyone, respectively. While doing this, you will get a few other trophies/achievements on the way, such as Ghost , Specter , Faceless , Surgical and Vanished .
Basically, you should try to get every trophy/achievement that doesn't involve killing someone in this playthrough, although it's best to avoid doing the side missions for Granny Rags. This is because the last part of it can be glitched (avoiding spoilers). You still have to do Slackjaw's side missions, since he will take care of some of the key targets in a non-lethal manner.
High Chaos Playthrough
A High Chaos playthrough requires you to kill a lot of things, so you should be killing everyone and everything you come across. You can do it stealthy or you can just go straight in and murder everything, although you'll likely need a lot of health vials for that. It's ideal to do the Mostly Flesh and Steel trophy/achievement for this, as you might not need to sneak around and you don't really need to use your powers outside of Blink.
Since you'll most likely be avoiding using powers on this playthrough (if using the suggestion above), then any trophies/achievements involving those can be done in a clean-up after doing the two initial playthroughs (via Mission Select). If doing Mostly Flesh and Steel, you can buy equipment and get Bone Charms to help you out.