Here are a bunch of tools that could be useful to cubers.
- qqTimer - timer with a ton of features, including dozens of scramblers
- Algorithm Mirrors - finds mirrors and inverses; update of strangepuzzle's program
- Rotation Remover - removes rotations from an algorithm
- Order Calculator - finds out how many times you have to do an algorithm to get back to solved, supports 2x2 through 5x5
- Square-1 Cubeshape Trainer - practice more and more difficult cubeshapes
- Square-1 EP Optimizer - for people learning edge permutation, figures out which algs you can learn to save time on the most solves
- ksolve+ - C++ program that searches for algorithms for arbitrary puzzles
And here are some cube simulators.