Gunther seems like he should be more popular, especially since Gunner and Gunnar are in the top 1000. However, in 2015 the name Gunther was only given to 26 boys, and that is only a slight increase from the handful of years before. It has been in use since at least 1924 in the U.S., but in native Germany (where he's pronounced GOON-thur) this name is very well known, usually spelled Günther. Guenter, Guenther, Gunder and Gunter have also been used.
There are several namesakes for the spelling Gunther, including fictional namesakes. The 5th century king of Burgundy was a bit of a legend, his story told in the Germanic saga Nibelungenlied. Another interesting story is that of Gunther of Bohemia, a Catholic hermit and saint from the 11th century. One more famous namesake was Gunther of Cologne, an archbishop who died in 873. He was from Frankish nobility, but for a long time was not very popular.
Simplified, Gunther means "warrior" in Germanic from the elements gund or gunþiz, meaning "battle," and hari, meaning "warrior, army." (No, it doesn't mean "bold warrior," but maybe it could be taken to mean "battling armies.") It comes from the Old Norse name Gunnar, meaning "strife." So the original form is the one currently in the top 1000, but they are cognate.