Was thinking about this earlier today.

Mercury had no real numbering system that I'm aware of (I'm sure it did, I'm
just not aware of it).
So you had Faith 7, Hope 7, etc.

Gemini basically used roman numerals.
Gemini VI, X, etc.

Apollo had 3 that I'm aware.
Apollo 4, 6, 8, etc.
AS-201, 204, etc
SA-201, 204, etc (i.e. the same as above, but different centers put a
different emphasis on the "lead" vehicle")

Shuttle:
STS-1, 2, etc
STS-64B

What else?