If you have a theft objective, check your PDA message list or a crew manifest (if available) to figure out if someone is likely to be near whatever it is you need. Hack an out-of-the-way door to find the power wire if you don't plan on using an emag (personally I think that pulse-crowbarring works better, because people won't notice a bunch of open airlocks). You can also build hidden doors into the place you need to access. Note, though, that this works best with no AI. Basically unless your objective is in a relatively secure area that is actually staffed, you can stealth easily.
For assassinations, my go-to is parapen to choke while dragging them into a tunnel or back room. Make sure to strip their radio and jumpsuit as soon as you can, and then move elsewhere. If you can, use the incinerator or gibber to ensure permadeath. Otherwise your best bet is probably going to be hiding the body in an out-of-the-way locker, as spacing can potentially result in the body ending up somewhere that someone will see it. In terms of technique, don't just run up. Start a conversation away from other people and say something that should require a lengthy response, then pen them while they're typing.
Other than that, the most effective is probably going to be doing Toxins (if you can make a decent bomb) and planting them around their workplace. Even a couple mediocre bombs can completely wipe out a good section of the station if used together. You have a couple options here: timers are the worst. I prefer remote-detonation and simply waiting until I see them go in, but planting a proximity bomb in a locker that they use frequently could also be viable. Just make sure that if you're using remote-detonation that any bombs you aren't planting are set to a different code and frequency.
If you don't care about being obvious just murder the fuck out of them on the escape shuttle and cause as much havoc as possible.
Incidentally, if you're looking for a good place to blow up as a distraction, the morgue is close enough to genetics that you could probably break cloning with a couple decent bombs. If you're going the mad scientist traitor route, it can be viable to R&D up to bags of holding if there are miners, so that you can carry a satchel full of bombs inside your backpack. When you're planting bombs, avoid leaving them in the open. Put them in lockers, crates, and in the extra backpacks you can get from the personal lockers in the locker room. If you're planning on remote-detonating them but have a risky drop sequence, set them along a range of frequencies in case you need to detonate them before they're all planted and you don't want to waste whatever is left in your bag.