I like that we mention Rally story numbers and defect numbers in our standups where I work.

I had a formal training on Scrum at FramesDirect in which we were explicitly told not to rattle off esoteric encodings that no one can follow (story numbers) in a standup as no one can follow what you are talking about. This isn't really true if you mention the number and then explain what it is and I think it does help out in talking about the story. If not everyone in the standup, a few others will recognize the story by its "name" as especially so if you follow it up with an explanation of what it is for the rest of the room. With the convention of cares about the numbers and emphasis on them comes, in my opinion, an easier time in using both Rally and source control.