For a complete index of Math HTML5 sims by topic see PhET Sims – Index.
Trig Tour is one of the excellent HTML5 Math PhET Simulations from The University of Colorado Boulder. There are numerous PhET simulations covering Physics, Biology, Chemistry, Earth Science and Mathematics. Note the collection of HTML5 versions which will work across all platforms and devices.
For an excellent introduction to Functions the PhET Simulation, Function Builder provides a very visually appealing resource. Using the pattern option even very young students could explore important concepts. This is very intuitive to use, the slides in the following slideshow demonstrate examples of its use.
PhET Balancing Act working nicely on my phone!
Staying with Mechanics, one of my favourites now available in HTML5 collection: Projectile Motion.
For Algebra we have some lovely simulations – really clear demonstrations.
Area Model Algebra is very simple to use. Rectangles of various sizes can be built showing the relationship between multiplication and area.
The ability to display or hide the variable and to take snapshots means working can be clearly shown.