For anyone who's wondering what the best score you can realistically get in this game is here on Newgrounds... it's probably something like this.
I normally play this on my computer at home, which is very fast. The other day I played it at work and found I could more reliably get a solid score, because the computer runs slower and I have more time to think. Took it right down to the wire this time. My score going into the final boss fight was 3.32mil and I'd only been hit once, so I was able to sacrifice some hits in the name of finishing the game.
Then, today I played at home again and after a spectacular first Act (877k going into the first boss) I got the score below, taking over 3.35mil into the final boss fight with plenty of time to spare. This game is addicting!
Feb 11, 2010 edit: Just played it again and increased my score by almost 10,000, bringing my new all time best to what you see below. Entered the final boss fight with 3.36mil and 6 hearts to burn, and got my final level up after destroying the last red circle cannon on the right armature of the final boss. I wonder if I can hit 6.2mil...
I guess you can set this game next to Paradox Embrace for medal games I totally own.