Let's say that you need to send your friend a message, but you don't want another person to know what it is. You can use a full-blown encryption tool, such as PGP. If the message isn't that important or if it is intended to be decrypted by hand, you should use a simpler tool. This is a page dedicated to simple text manipulation tools, which all can be replicated with just paper and pencil.
If you know of another cipher that you think should be on here or a tool that would be useful, request it and perhaps it can be added to the site.
Codes and Substitutions
Replaces a letter with another letter or a set of symbols. This is the most basic way to hide a message because the translation of the letter doesn't ever change. There's not much to configure here. At most, you will select an alphabet, possibly key it, and maybe select an option for how the algorithm works.
American Sign Language - These are the hand signs one uses to finger spell when a more advanced sign isn't known.
Atbash - A very simplistic cipher where you change A to Z, B to Y, and so on.
Base64 - This is typically used to make binary data safe to transport as strictly text.
Binary - Encode letters in their 8-bit equivalents.
Dancing Men - Sherlock Holmes solved a mystery that used a stick man cipher.
Flag Semaphore - Signaling messages using flags, often from ship to ship.
Gold Bug - A substitution cipher from an Edgar Allan Poe short story.
Lego Bionicle - Different letter sets used in the Lego Bionicle world.
Letter Numbers - Replace each letter with the number of its position in the alphabet. A simple replacment method that is usually the first one taught to children and is still an effective way to obscure your message.
Morse Code - Once used to transmit messages around the world, this system can still be used in certain situations to send messages effectively when alternate mediums are not available.
Pigpen - Old substitution cipher, said to be used by Hebrew rabbis and the Knights Templar.
Rot13 - Swap letters from the beginning of the alphabet with the letters at the end of the alphabet. Encoding is the same as decoding.
Spirit DVD Code - The Mars rover has a DVD with a code printed around the perimeter.
Webdings - See your message in a set of symbols
Wingdings - Hide the text using icons instead of letters.
This may shuffle letters around in order to obfuscate the plain text. Alternately, it can encode letters into different letters using an algorithm so one letter in the cipher text could be any number of letters in the plain text. Typically, these have more options and settings, allowing a single algorithm to apply to the message in a variety of ways.
Affine - Similar to a Caesarian shift, but also adds in a multiplier to further scramble letters.
Baconian - Used to hide a message within another message by using different typefaces or other distinguishing characteristics.
Bifid - Breaks information for each letter up and spreads it out in the encoded message. An easy and fairly secure pencil & paper cipher.
Caesar - A Caesar cipher lets you add an arbitrary value, shifting each letter forwards or backwards. Traditionally, the offset is 3, making A into D, B into E, etc.
Columnar Transposition - Write a message as a long column and then swap around the columns. Read the message going down the columns. A simple cypher, but one that is featured on the Kryptos sculpture at the CIA headquarters.
Double Columnar Transposition - Because two is better than one. This was used by the U.S. Army during World War II.
Gronsfeld - This operates very similar to a Vigenère cipher, but uses numbers instead of a key word.
One Time Pad - A virtually uncrackable cipher that relies heavily upon a random source for an encryption key.
Playfair - This cipher uses pairs of letters and a 5x5 grid to encode a message. It is fairly strong for a pencil and paper style code.
Rail Fence - A mildly complicated one where you align letters on different rows and then squish the letters together in order to create your ciphertext.
Rotate - This acts as though you are writing the letters in a rectangular grid and then rotating the grid to the left or right 90°
Skip - To decode this, you count N characters, write down the letter, count forward N characters, write down the letter, etc. It is used for section 3 of the Kryptos.
Übchi - A double columnar transposition cipher that uses the same key, but adds a number of pad characters. Used by the Germans in World War I.
Vigenère - Based somewhat on the Caesarian shift cipher, this changes the shift amount with each letter in the message and those shifts are based on a passphrase. A pretty strong cipher for beginners. Functionally similar to "Variant Beaufort" and this also supports autokey.
Analyze - Shows how often certain letters appear in your text. Used primarily to assist in decryption.
Cryptogram Solver - If you have a plain text message, this will help find possible solutions in a matter of seconds. It works with simple substitution ciphers only.
Cryptogram Assistant - This helps you manually solve simple ciphers, which are methods where you replace one letter with another.