The forced crash report showed that there were quite a lot of zombies about. I opened up the world in MCEdit and deleted all nearby entities and the lag disappeared. I don't know how to be more selective and delete only zombies to check it was them and not any of the other entities, or anything unrelated that also gets modified by MCEdit (it relights modified chunks, I have no idea what other changes might've occured) but, erm... could it be related to 49 zombies converging on a village?

Forced crash report attached.

I've been getting this at times too. Attaching a world save in case it helps with replication. I'm in a desert blacksmith, the chest in there my inventory has some dirt and sand blocks. I can place them without a problem, but on breaking them, they reappear for about a second before disappearing and dropping an item. I have rebooted my PC and used a different MC account, but with both the lag persists. Non-default settings in this world are largeBiomes generator, gamerule naturalRegeneration false, scoreboard objective deathcount, displayed in slot_0. The scoreboard and regen were set using NBTExplorer rather than commands, but I was able to play for quite a while after doing so without lag. The other lag I've noticed is the moon rising a bit then getting set back, resulting in time passing more slowly. I'm getting a framerate of about 50fps, and I can't see from Shift-F3 what's causing the lag.

Edit: using snapshot 13w24b

Block lag is when you break a block with an axe or pick and it takes several seconds to break into a particle you can pick up after the “block breaking” sound had occurred. I hope that clears it up. The lag has returned but it is not quite as severe yet but it seems to be worsening.

What is "block lag" ?