1. By a senior addressing a junior. For example, Takashi Sugiura might address someone like Junta Miyawaki as "Junta-kun" or "Miyawaki-kun". Miyawaki would however never address or refer to Sugiura as anything other than "Sugiura-san", which literally means "Mr. Sugiura" as Sugiura is not junior to him.
2. When fans use it, it is used as a term of endearment. It's hard to explain as there is no equivalent in English. It's a little more formal than using the suffix "chan" (i.e. "Ken-chan", "Kat-chan", which are used for nicknames, Marufuji has called Sugiura "Sugi-chan" and YO-HEY refers to himself as "YO-HEY-chan" occasionally), so I guess it can be almost seen as the most you can get away with and a middle ground between "chan" and "san". Some fans put the word "kun" on nicknames for wrestlers i.e. Ken-Kun (KENTA). It is not something that fans would ever address someone like Kenta Kobashi with however.
3. It can be used between people of the same age group, and you may sometimes hear men address their peers with it.
Why Naomichi Marufuji & Kenoh use it.
As stated above the suffix "kun" in this situation is used by a senior to a junior, and Marufuji and Sugiura sometimes address Kenoh as "Kenoh-Kun" (or Ken-kun) to show the fact that they are his seniors. Kenoh, however, uses it back to them as a mark of (kayfabe) disrespect, as in reality he wouldn't be addressing them as this or referring to them as that in conversation. In the case of Marufuji and Sugiura addressing Kenoh as it, its almost as if they are patting him on the head and treating a grown man like a small child, or else a small child who is playing make believe that he runs a bank or something. Kenoh uses it back to them, "Marufuji-kun" in particular, like he is addressing him as "junior".Daisuke Harada addressed Yoshinari Ogawa as "Ogawa-kun" (which ironically mimics the heavyweights, who Harada hates), which is an act of supreme cheekiness as probably no one has called Ogawa that since he was a trainee in All Japan.
