A good practice is to NOT edit the code in common_files ever - instead apply the technique that Mike discusses in his video:
http://www.youtube.com/watch?v=5nkd7FPHMdA
I typically will comment the daylights out of my templates -- because you just may revisit something a few years from now and you will think, "WTF was the coder thinking?" -- but I can see in the comments that I was the freaking idiot that did this...
Where this technique becomes messy is if you are purchasing 3rd party mods -- and the 3rd party wants common_files template edits. SO you have to work around that.
The idea that "I'll leave the commented out code in-place just in case of a future upgrade" is a myth. If you're upgrading, you are starting from scratch with new core. Your edits may or may not be useful. But the idea that you can upgrade any template file that's been well modified or commented out is, well, fantasy. It doesn't really matter what you do to the templates.
NOW -- php files -- comment the daylights out of them too... but like templates, all the commenting in the world will not solve your upgrade challenge if you ever upgrade. But commented files are better than nothing.
Good luck!