Lava Carefully place a bucket of lava by your victim innocent bystander.
Once they are aflame, pick it up again so it doesn't spread too far!
Fire Light them on fire with flint & steel.
You can punch out the flames immediately to minimize collateral damage.
Suffocation
Carefully dig a hole directly beneath them, and fill it in with sand/gravel.
Drowning Construct a water flow that drowns them
(look up some mob traps). '
Accidentally' knock them into it.
Zombie
Apocalypse Got access to a zombie spawner? '
Pipe' your zombies with water flows into the center of the village.
Unless they've got an iron golem, there may be a few casualties.
Remember:
It's not you, it's the hostile environment.
gaming.stackexchange.com/users/3610/fredley
I just tested these two options in my village right next to an Iron Golem, and he didn't bat an eye... Use a flint and steel to light the spot on the ground below them on fire, being careful not to hit them by accident.
Then just let 'em burn.
Oh, and be careful not to set anything else on fire when you do it.
If anything else nearby catches, just punch it to extinguish it.
You can gently nudge villagers where you want them to go, so you could dig a 2-block deep hole next to the "mark", nudge them into the hole, then quickly drop a couple of sand or gravel blocks down on them from above to suffocate them.
gaming.stackexchange.com/users/15/gnovice
You may need to exercise even more caution now with the pretty scary update, or your villagers won't reproduce after other villagers have "accidents.
" From the version history: After a villager dies to natural causes, excluding mobs, while a player is within 16 blocks or if a mob kills a villager, no baby villagers will be produced in the next few minutes ( http://www.minecraftwiki.net/wiki/Version_history#1.4.2 ) You may want to send less useful villagers to serve out the rest of their lives in iron golem farms, or you could create some "death rails" for sending villagers who have outlived their usefulness 20 blocks away from the village to "a place where accidents happen" Keep in mind that with the update and village reputation you'll want now more than ever to avoid direct involvement.
Gary's mantra rings true: Remember:
It's not you, it's the hostile environment.
gaming.stackexchange.com/users/35504/jlsecrest
If you want to have even more fun: make LANDMINES
:D
This is an effective way of both killing the villager and enjoying yourself as you watch the explosion.
For even more bonus points, gas leaks in houses are a common 'accident'.
gaming.stackexchange.com/users/35540/Wijagels
My strategy is to dig a deep hole then put a TNT two blocks down and gravel/sand on top, then a pressure plate.
When they step on the plate, they trigger the tnt and fall with the gravel/sand.
They'll die either from the fall or from the explosion.
gaming.stackexchange.com/users/80802/KKage
One strategy, is to get dirt blocks, sand, a door and trapdoor.
Use the dirt to build a tube and an extension to put a door.
So the villagers don't open the door, use the trapdoor(s) to lock it[make sure the trapdoor isn't in the tube].
Punch, wait or fish villagers in the tube, then lock it in place.
Put a dirt block over the villager, then put two sand blocks on the dirt block placed above him.
Then break it two kill the villager.
The dimensions for the tube is 3x3 and surround the outside walls except the center block.
A funny way to kill the darn villagers with crappy trades, who trade crap.
gaming.stackexchange.com/users/126936/Malachite
Try making a mine cart and track and put a 4x4 5 block deep hole at the end of the track.
Surround the 4x4 hole with blocks except the part where the track will end.
Then lead the track up to the hole with lava (the section where there’s a hole).
Then whenever you need to kill a villager just push them in a cart and off
they go( make sure the second piece of the rail is powered by red stone).
gaming.stackexchange.com/users/237474/Joshua
I have a populous village now but I am not interested in the villagers' trading options. I'd like to make sure some of them have an unfortunate "accident" so they can be replaced.  Obviously CSI: Minecraft can't draw anything back to me lest I feel the wrath of an Iron Golem or two.  How can I pull this off selectively (i.e., as specific to a villager of my choice as possible)?
How can I make a villager have an... "accident"?
gaming.stackexchange.com
<minecraft-java-edition>
gaming.stackexchange.com/questions/80519
gaming.stackexchange.com/users/190/fbrereto
Light them on fire with flint and steel. You can also use drowning, lava and landmines. There are plenty of ways to cause an accident at villagers, such as make them suffocate with the help of sand or gravel.
The community suggests few ways to cause a villager having an accident.