I just hope that I could find this feature earlier. TikZ
Some nice examples to start with:
- Neighbourhood definition
- Highlighting elements in matrices
- Signal timing
- Body plot of functions
- Database decimation process
- Flowchart with block highlights
- Set operations
- Cross-comparsion among curves
- Phasor diagram (more fancy)
- Difference quotient (partial zoom-in)
- Nested Grids
- Digital Signal Processing Library
More examples can be found in the official site, Graph Theory in LaTeX 2, Drawing Trace Diagrams, and TikZ tutorials.