Minecraft – How to find the location of a given item by looking at the world data

As far as an in-game (i.e. "not cheating") solution, the only real guidance I have found is this line from the Minecraft Wiki:

They only occur in the plains or desert biomes.

So that's where you should limit your searching to, probably around the edges of the deserts as this image shows:

Another alternative listed in the "Finding NPC Villages" section of the wiki involves making a superflat version of your map (using your map seed), then flying around in creative mode. As noted, however, this can give you many false positives (i.e. villages that spawn on the superflat map that wouldn't spawn on the normal map due to the presence of a non-flat biome).

Options outside of the game, as listed in this answer about finding strongholds, would be to use cartography programs to inspect your map for tell-tale blocks that you might see in villages. Good indicators might be:

• Bookshelves or crafting tables, which show up in village libraries.
• Pressure plates, which are used to make tables in houses and shops.
• Furnaces or iron bars, which show up in village forges.
• Many rows of wheat.

Unfortunately, it appears the answer is "you can't, or at least not without spending a prohibitive amount of time on the investigation, and even then you won't be sure of anything."

If someone finds a solution that's less time-intensive, I'll happily accept it instead of my own bleak conclusion. But after a lot of research I suspect there isn't one. I've updated the question to clarify that solutions ideally won't require hours of tedious manual work or monitoring.

I appreciate the answers that have been submitted so far. Unfortunately, manually searching everywhere for a stolen item would be too time consuming, and even upon finding it you couldn't be sure who put it there; it would be easy for a thief to frame someone else. And watching a potential crime spot continually until the crime happens would take too long since there are several possible griefers, many locations that could be griefed, and thefts are often spread out in time.

So for the time being the answer seems to be:

1. Use the techniques that I outlined in my question, whether using InvEdit to inspect player inventories, or else manually copying their [username].dat files to inspect inventories and Ender chests. If it's in their inventory or Ender chest, there's no question who took it.
2. Or give up and install Bukkit or Spigot and an anti-griefing plugin like WorldGuard or Prism.

We switched hosts and installed Spigot and Prism, and it was 100% worth the effort. Spigot runs even faster than Vanilla Minecraft did, and Prism is awesome for tracking down offenders and reverting their evil deeds.