getbootstrap.com/customize - The original Bootstrap theme customizer - input values for everything.
Bootstrap Magic - Input values for variables and see effect in real time; can export Less variables or CSS.
Bootstrap Live Customizer - More complete options, including panel colors
PaintStrap - Set of 7 color variables only
BootSwatchr - Edit variables.less and see effect in real time in sample page, but you have to know (or spend time discovering) where the code lines and page objects are. Can export Less and CSS.
StyleBootstrap - Site was offline on a January 23, 2016 check.
Visigene - Simple visual editor but pretty thorough effect (panels, etc. are styled).
...and more. If these don't seem to work correctly in one browser, try another.