ASCII Code
Morse Code
ITA2 (Baudot)
GoldBug
Talletic
Baconian
Kennyspeak
Telephone Keys
Bar Code Numbers
Simple Substitution
Cryptogram (Aristocrat)
ROTx (Caesar Cipher)
ROT ASCII
ROT47
Atbash
Affine
Vatsyayana (Kama Sutra)
Dvorak keyboard code
Columner Transposition
Double Columner Transposition
Railfence
Redefence
Patterson/Jefferson
Chaocipher
Vigenere
Autokey Vigenere
Keyed Vigenere (Quagmire IV)
Beaufort
Porta
Gronsfeld
Alberti
Trithemius
Larrabee
One Time Pad (XOR-ITA2)
Running Key
Playfair Cipher
Bifid Cipher
Trifid Cipher
Four Square Cipher
Polybius Cipher
Nihilist Substitution Cipher
Bazeries Cipher
ADFGX
ADFGVX
Pollux
Straddling Checkerboard
Monôme-Dinôme
Fractionated Morse
VIC Cipher
Enigma
Lorenz SZ40/42
Hill Cipher
PGP (OpenGPG)
RSA
Computer Encryptions
Hash Generator
Brainf**k
Ook
Moo (Cow)
Number Bases
Number Bases (2 to 62)
Geocaching GCBase31
Base64
Base32
Base58 (Bitcoin base)
Adobe Base85 (ASCII85)
Base91
UUencoding
Geohash
What3Words
Convert coordinates
QuadKey (Bing Maps)
Steg Detect (RGB)
Steg Detect (Geocaching Toolbox)
Steg Detect (End of File)
Steg Detect (Image text)
Exif data
Image colour table
QR/Barcode Decode
QR/Barcode Create
Check prime numbers
Resistor Colour Codes
RegEx functions
Cross sum calculations
ISO 3166 Country Codes
Roman Numerals
Basic Analysis
Substitution Analysis
Transposition Analysis
BiGram Analysis
XGram Analysis

Links to usefull web sites for geocaching, especially mystery caching.

Cipher Types described by the American Cryptogram Association. A great source of information for understanding the workings of the ciphers (highlighted ciphers are inplemented in the Mystery Toolbox. = passed ACA test cipher)