It's possible to change Leopard's 3D Dock to a more Tiger-like 2D version using the following Terminal command:
defaults write com.apple.Dock "no-glass" -bool TRUE; killall Dock
That's what I did, and the small bluish-white dots below the icons of running applications become much more obvious.
I don't know if that's one of the TinkerTool tweaks you're referring to, but I know it's among the Dock settings accessible using OnyX.
