Software for manipulating scales and tunings

Scala - the de facto standard software for creating, manipulating and analyzing tunings
- Wikipedia article on Scala
- instructions for Creating Scala scl files for rank two temperaments
alt-tuner - a tuning plug-in that does adaptive tunings, on-the-fly retuning, and scale analysis by Kite Giedraitis
Temperament finder - site by Graham Breed
Tonescape - Music composition, analysis and educational tool by Joe Monzo
Fractal Tune Smithy & Bounce Metronome - by Robert Walker
Scala to TUN and MTS online converter - by MicrotonalSoftware.com

Browser-based tuning tools (JavaScript etc.)

Interval calculator - a nice online interval calculator tool, shows linear fraction and EDO fraction expansions, too
Animated MOS ring demo
Hexagonal Keyboard Demo - by Sjoerd Visscher
edjiruler v0.0.1 - Visualize JI intervals close to equal divisions of whole numbers
Scale Workshop - Generate tuning files in your browser
Rank 2 Regular Temperament Generator - generate rank2 regular temperaments
MOSedo - Moments of Symmetry in equal divisions of the octave calculator
Harmonic Entropy Calculator - Interactive Harmonic Entropy curves.
Online H-System Calculators - Hunt Intonation Quality Grade Point Average (IQGPA) Calculator
Microtonal Software Scale Tree - ET Scale Tree Playground
Offtonic Microtonal Synth
Wickisynth - tuning demo synthesizer with Wicki-Hayden key layout
Online 19-edo keyboard
Online Terpstra keyboard (isomorphic hexagonal keyboard)
Microtone - A HTML5 uniform keyboard demo with any equal temperament
The Monochord - Try out just intervals from a base frequency.
Rational Keyboard - JI keyboard with keys that grow in size
Tonespiral - Listen to harmonics visualized as a spiral
Wolfram Alpha Regular Temperament Widgets
Just Intonation -> EDO calculator

Cents to Ratio Calculator - and much more! Also, another one with extensive instructions.
Fraction Expression Calculator - easily do ratio arithmetic
Continued Fraction Calculator
Fast Decimal to Fraction Approximations
Least Common Denominator of Fractions (LCD) Calculator - put your JI ratios in here!
Octave - a free, open source equivalent to MATLAB; useful for working with matrices and much more
Wolfram Alpha - perform a variety of intensive mathematical calculations in your browser
Online LaTeX Equation Editor - create mathematical expressions in LaTeX format for wiki pages etc.