Currently I use two different ones in my math classes. One is Geoboard for the iPad. It is just like the real life geoboards we have in our classrooms except this app comes with two different boards and lots of colored rubber bands but no chance of loosing either the board or the rubber bands. I've used it for students to create various types of triangles such as those classified by sides, or angles, finding the number of triangles in a polynomial as a starting point to find the equation telling the interior measurements of the angles, tessellations, transformations, etc. If you use a geoboard in real life, you can use this app to do the same thing.
The second app I've used in geometry is Geometry pad. It allows students to use a coordinate plane for geometry. It allows students to make all sorts of quadrilaterals and polygons, triangles, circles with radius, arcs, chords, etc. There is an option for points, angles, lines, rays, segments, perpendicular bisectors, medians, altitudes and angle bisectors. you can draw, type, use a ruler, and do certain functions. I've used this one when the book has a coordinate plane problem, transformations, midpoints, diagonals, etc. If I have to resort to worksheets for certain activities, I will have my students use this app to help them complete the worksheet.
Due to iPads not having java, I am unable to use many of the virtual manipulative websites on the internet. I found another app that has great ratings and I hope to down load it tonight to play with. Its virtual manipulatives and focuses on decimals, percents and fractions. Although it is rated for middle school, many of my lower performing high school students are weak in that area. I think this could be used in that class to help them learn how decimals, percents and fractions relate to each other. I hope to give more information on this app on Monday or so.