Red - for additions or corrections
Yellow or Green - for items checked and verified
Blue - for notes and questions (traditionally this was a special pencil used so that when the drawing was duplicated on a xerox machine it didn't show up)
If you make a mistake you can write STET next to the item. It means "let it stand."
[ref: http://www.aps.anl.gov/APS_Engineering_Support_Division/Design_and_Drafting/DDStandards/DDStandards.html]