Mathematica isn't often used for CTFs, but it is actually a pretty good choice for cryptography and stenography challenges. And many students can get a free license through their university.
Mathematica can import many many image and audio formats with Import[]. Additionally it has very good support for matrix manipulation, modular arithmetic, and symbolic computation.
- LSB image – Least significant bit (LSB) image analysis.
- Pixel data – Pixel data and file formats.
- QR code – Barcode recognition and simple list/matrix manipulation.
- Coordinate plotting – Plot coordinates from a SQLite database.
- MIDI notes – MIDI note analysis. Manipulate[] example.
- Spectrogram image – Audio spectrogram image.
- Morse code – Sound channel manipulation, data decoding.
- Hill cipher – Hill cipher implementation.
- Rabin cipher – Compromised Rabin cipher implementation.