There are several structures added by Thaumcraft 3, which usually have good loot guarded by Wisps or monsters.
Greatwood trees sometimes have hidden spider nests under their roots. These spiders protect a treasure chest with basic dungeon loot. These trees can be easily identified by the spider webs in their leaves.
These can be found scattered all across the world. They consist of 2-4 Obsidian Totem Blocks, and an Obsidian Tile as the base.
A circle made up of Obsidian, Obsidian Totems, and Obsidian Tiles. In the center is a chest with very good loot, ranging from Knowledge Fragments to the Shovel of the Earthmover. However, underneath the chest is a dangerous wisp spawner, making it a difficult, but worthwhile venture.
Found in NPC villages, this tower is the home of a Wizard. You can rob the wizard's home and steal his magical artifacts, or trade with him if you want to be nice.
These hills contain a dungeon whose entrance is blocked by iron bars. If you dare to enter, you'll have to defeat Wisps, Zombies, and Skeletons to get the loot, which includes Knowledge Fragments, Thaumium, and Enchanted Books.