There are several structures added by Thaumcraft 3, which usually have good loot guarded by Wisps or monsters.
Spider Tree
Edit
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.
Obsidian Totems
Edit
These can be found scattered all across the world. They consist of 2-4 Obsidian Totem Blocks, and an Obsidian Tile as the base.
Totem Circle
Edit
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.
Wizard Tower
Edit
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.
Barrows Hill
Edit
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.