Update (December 27, 2013): This site has been offline for quite a long time.
Manipula Math with Java is a Japanese website that has an excellent collection of Java applets that can be used for teaching and learning mathematics. There are 279 applet collections divided into the following categories: Middle School, Trigonometry, Vector, Calculus, Complex Numbers and Conics.
The site also contains Java Lessons for Creating Simple Java Applets.
Last year, I have shared about an applet for visualizing isometric views. I found another superb 3d math applets site, Maths.Net, through Great Maths Teaching Ideas. Maths.net includes applets for exploring prisms, nets, platonic solids, and other 3-dimensional objects. It also includes an applet for building polyhedra.
My favorite applet is Guess the view. It lets guess the isometric view of a particular solid.
It turned out that the applets in Maths.Net are also from Wisweb, the same site where I discovered the isometric views applet.
Math Plotter is a site containing a collection of Java Applets and interactive materials that can be used in teaching and learning mathematics from high school to graduate courses. Math Plotter includes applets for geometric drawings and constructions, graphing functions, plotting statistical data, and exploring solids.
The site also contains GeoGebra applets and resources. Math Plotter is a project of Laurenceville High School, New Jersey, USA.