Every time I reset my Arduino, the little yellow LED next to pin 13 flashes a few times... it's not that I mind the blinking, but pin 13 is directly connected to a shield I built and the initial pulsing is messing up my circuit. Is there a way to stop this? I can post my code if needed, but I don't think it's the problem (this happens regardless of the uploaded sketch).
You could tweak the fuses to stop it using the bootloader. That would require an external programmer (eg. another Uno). Then it instantly goes into your sketch. The relevant fuse is the BOOTRST fuse.
And of course, you could no longer use the bootloader to upload your improvements. It could be a viable option if you are sure you don't need to change it for a while.