I run a small 3.3.5 server for a group of friends and have wrestled with balance issues too.. At first, I tried scaling player damage and healing in the server's c++ code, and changing database entries to tune the bosses. It worked, but maintaining it was more work than I wanted. What I finally did was modify Spells.dbc to add a new buffing aura spell along the lines of Wrath's "Strength of Wrynn", which gives players a percentage increase to damage, healing and health. I actually just copied "Strength of Wrynn's" dbc entry into a new spell, and messed with the percentages till it felt right. To allow raiders to use the new spell, I modified a database item to cast it, and gave the item to the raid leader. No large scale db changes, no code to maintain, and it's pretty easy to tweak the numbers to your liking. I'm sure something similar can be done in vanilla.