Webquests about cells, cell organelles, the differences between different types of cells, and other good biology stuff. These are usually geared towards high school students.
Webquests about the Periodic Table of Elements. These cover the gamut from elementary to high school. Anything related to an element, classification of elements, characteristics of elements, etc.
Webquests about volcanoes. This is a pretty popular topic. A lot of these are geared towards younger kids, although it's certainly a topic that could be addressed in middle or high school.
Webquests about the solar system and the planets. This is usually a topic covered in elementary or middle schools, and most of these are geared towards younger students.