There is a default preference I want to edit (or delete and recreate in the English.lproj) in the Dock bundle in System/Library/CoreServices.
What are the possible negative repercussions to editing these app bundles?
What's the worst that can happen?
1) You break something and have to safe boot or target mode boot to put the original file back in place? You have to have a short term plan to fix things.
2) You forget you edited it and some system update or process changes and the mac crashes later? No worry if you have backups (running Time Machine keeps you an hour or so of lost work plus whatever time you lose realizing, fixing and restoring from the last backup) You might lose some time scratching your head later, but even though it could ruin other data, it probably would just be a crash or an error that would be obviously wrong and you'll eventually remember the change you made.
Protect yourself, get a second boot drive ready, and have at it would be my advice.
I've had my Dock.app modified since the launch of Leopard to customize the dock's appearance, with no downsides. I've reapplied the same hack to Snow Leopard, and now Lion.
I'm just replacing a few .PNGs, but my experience has been that it's really not a big deal.