Too many operations: When a plugin spawns too many entities, or attempts to perform complex tasks on events such as movement, you will begin to see lag. You will see this a lot when loading up large MagicSpells configs, or using permissions systems that use YAML instead of a proper database such as PEX and GroupManager. Many plugins do this and do not take precautions against how, when the databases become bloated, the processing time will affect the servers tic. Flat files as a database: When you have plugins that use large files to keep track of lots of data iterating through that file or in memory depending on how it is stored will take a long time. A few examples would be some PVP flags or Glow plugins which will continuously read from player files. File usage: Any plugin that is constantly reading from player files, especially on events such as movement, damage or interact. There are many things that can cause lag but a few of them will be the most likely culprit for most servers. Any lower than this and you will begin to see lag. This can go as low as 55.55ms for 18 TPS with minimal issues. Ideally each tic should take no more than 50ms to maintain 20 Tics Per Second (TPS). The world will not update, players will not appear to move and entities will be frozen in place. 
This all occurs on one thread, and the next loop cannot start until the current one finishes. When the server goes to tic, it runs through every TileEntity update, entity update, block update, events and other processes until it's done. Minecraft server software all operate in a similar matter with one key problem: there is no multi-threading or timing limits for the main game loop. The key to understanding what is causing lag is to understand how Minecraft works.
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