Is there a way to pinpoint lag source?

[VideoBoy]

I logged in today to find my server static at 3tps with only 2 players on, where I normally get at least 15tps on a full server with 20 players. Lag wasn't that apparent except mobs walked & targeted players very slowly, and IC2 machines were being snails.

This isn't the first time. The only way to fix it is doing /stoplag and then /stoplag -c (a WorldEdit command) to get it back to 20tps. This kills every farm animal so I get a lot of pissed off players. Is there a way to pinpoint the problem? It's not flooding pipes because //remove items -1 didn't show a large number of entities. Neither did //butcher 1000000. NoLagg Examiner doesn't help because this isn't a plugin issue.

Any help will be greatly appreciated. <3