1Special thanks to @David, for the great link he provided.
Seeing that this question has garnered some interest, And nobody has answered yet, I guess I'll take a crack at it.
After reading over the paper mentioned above, and researching other 2sources I decided I'd just compile a selected list of rocket and satellite name origins. This list is by no means complete, and feel free to add on if you know a certain spacecraft's name origin. I should mention that the paper above provides more than just rocket and satellite name origins, and I highly recommend reading it for yourself. With that in mind:
Agena: The Agena rocket is an upper stage that has its origins with the Lockheed Missiles & Space Company. The name "Agena" was proposed for the star Agena in the constellation Centaurus, because of the fact the Agena was an upper stage rocket, igniting in the sky.
Atlas: The Atlas rocket was a powerful first stage, used in various applications. In the early '50's, Karel J. Bossart, head of the design team at Convair (Consolidated Vultee Aircraft Corporation), Decied to ask his staff for name ideas for the then new Atlas rocket. In the end "Atlas" was chosen because the missile they were designing at Covair was going to be the biggest of any missile to date. Bossart named it for the Atlas, who, in Greek mythology, is a powerful God that holds up the earth.
Little Joe: The Little Joe rocket was a inexpensive rocket for testing the escape sequence of the Mercuy spacecraft. The rocket earned its name, because of its engine being drawn with four holes up, which resembled a "double deuce" throw, in Craps. The that type of throw is sometimes referred to as a "Little Joe".
Shotput: The Shotput rocket was
a rocket specifically made for testing balloon-satellite ejection
and inflation in space. It carried the Echo satellite payload. It gained its name from the fact that it "tossed" the Echo sphere above earth's atmosphere, in a vertical trajectory.
Saturn V: The Saturn V(Saturn Five) rocket, was the rocket used to place the Apollo vehicles in Lunar Orbit, as well as launch the Skylab projects into Low Earth Orbit. Nominations were submitted to NASA for the name final name for the Saturn V. The front runner for some time was "Krons", until the Committee suggested-Through the Assistant Administrator for Public Affairs George L. Simpson, Jr- The name "Saturn V". And Saturn V was chosen.
Redstone: The Redstone rocket has its origins as a battlefield missile developed by the U.S. Army. NASA went on to modify it and use it for launching sub-orbital Mercury flights. After having several Nicknames, the booster was officially named "Redstone" due to its development taking place in the Redstone Arsenal in Huntsville, Alabama.
Able: Since this name explanation was brief, I thought it might be best to directly cite the 1paper:
The Able upper stage was one of several derived in 1958 by the Department
of Defense's Advanced Research Projects Agency, Douglas Aircraft
Company, and Space Technology Laboratories from Vanguard launch vehicle
components. It was used with Thor or Atlas first stages. The name
signified "A" or "first" (from military phonetic communications practice
of stipulating key words beginning with each letter of the alphabet)...
Sphinx: The Sphinx Satellite was planned to be one of the smallest NASA satellites-Weighing in at just 113 Kilograms(249.122). It gained its name from a experiment acronym-"Space Plasma High Voltage Interaction Experiment."
Pegasus: The Pegasus spacecraft's most striking feature, is its impressive 96 meters wing span. In terms of satellites, is was the heaviest satellite to date. Thus being consider a "horse" sized payload. due to its massive wing span, and unprecedented size, the name "Pegasus" was chosen for the mythological winged horse.
Nimbus: The Nimbus satellite was named for the term "Nimbus" in meteorology meaning "precipitating cloud. Its name was Suggested by Edgar M. Courtright, Chief of NASA's Advance Technology Program.
Explorer 1: The "Explorer" name has its origins even before the birth NASA. before NASA was established, the name was used for US military weather balloons. Wilbur M. Brucker-secretary of the Army-announced the name. Its name reflected its mission, and the mark of the first US satellite.
Echo: Echo-an inflatable satellite, conceived by William J. O'Sullivan-gained its name from its mission- to be used as a reflector for radio signals. In radio terms, echo" is often used to describe the deflection of radio signals from earth to to an orbiting balloon. The satellite was thus named "Echo"
Note to contributors:
If anyone does deiced to add on to my answer, please make sure it's posted under the correct category. if a category does not exist, feel free to create a new one.