I used to have the Digital Color Meter (system app) in my dock, but since updating to Yosemite it doesn't appear in the dock anymore ("?" sign) Did they just move it and Dock cannot find it?
You can find it under Applications/Utilities.
From there, you can drag it to your Dock to create an alias. See Mac Basics: The Dock for additional info on making the most of the Dock.
To remove the Question Mark, drag it off the Dock until you see "Remove" then release.
If you're looking for something, e.g. an application, you can always press Command ⌘-Space bar to bring up Spotlight and start typing the name of the object you're looking for. In the case of an application, once opened and showing in the Dock you can control-click it and select Options > Keep in Dock if you with is to remain there, once closed.
You might find Mac Basics: Spotlight helps you find what you're looking for and Mac keyboard shortcuts interesting.