No matter how clean your code, there's something to be said for a fast, clean pre-launch cleanup with a reliable code formatter . My favorite by far is the HTML Formatter from LogicHammer.com: http://www.logichammer.com/html-formatter/
Complete with a full set of ColdFusion-friendly options, this simple tool makes cleaning your code a snap. I use it as I'm working, to clean up the work-so-far at any point, and before final launch to make sure the production code will be as easy as possible to maintain and revisit later on. It is a standalone executable, which means there's no installation, and you can put in anywhere you like on your hard drive.
I simply create a taskbar shortcut on my Windows PC and drag the files I want to clean directly from the 'project' view in Eclipse onto the icon - couldn't be faster, simpler or easier. I prefer to have my original files altered, with the originals automatically put in a specified backup location - you can also assign the option to leave the original alone and create a cleaned-up copy.
Among other fav features, HTML Formatter ships with a simple text-based config file which makes it incredibly easy to specify tags to ignore or to indent, and file extensions to be formatted or skipped ( you can run the formatting on specific files, or an entire directory).
For only $14.99 you get all the features and 2 years of updates (there is also an 8.99 version with a basic feature set). The program's developer has answered every question I ask directly and has been very helpful with customizations, even building in some features I requested a while back (for the record - I'm not affiliated with logichammer in any way, just very pleased with this slick little tool).