What I do is dig a 1x REAAAAALLY long hallway. Dwarves won't be taking this walk often (I hope) so it's unnecessary to make it pathing efficient. On either side of the hallway, I dig 1x1 rooms (1x2 if you count the space for the door). Coffin goes on that square, door separates it from the hall. All dwarves are assigned a coffin from birth/migration if possible. If necessary, I dig another paralell hallway with space for its associated tombs, and another, and another -- enough so I have as many graves as I have commoners, plus space to bury pets if someone gets upset about it (or the miasma), and room for population growth to get assigned tombs IMMEDIATELY. The crypts basically take up an entire z-level for advanced forts, with bigger tombs for dwarves of some distinction and the eternal cage prisons of goblin snatchers, walled up in living stone there to remain for all eternity (or, it used to have that until I learned you can pretty much safely mass-pit snatchers like everything else). The entire thing is also the first part of the fort to get smoothed and engraved, since it's huge, nice to smooth/engrave, and non-vital: perfect for training the engravers.
With necromancers upcoming I can just lock the doors of any filled tombs, sealing the dead in their eternal rest... unless necromancers can open locked doors, at which point harsher methods may be required. I started caring powerfully for the fate of the dead when I lost a fortress to delayed-action tantrum spiral. They came out of the losses from the ambush sad but sane and non-tantruming, but when their friends started ROTTING in the above-ground corpse stockpile, things got real ugly real fast.