Bowser Jr.'s mother

The identity of Bowser Jr.'s mother is called into question as early as his debut in Super Mario Sunshine.

During the events of the story, Bowser Jr. himself claims that his mother is Princess Peach, which she does not seem to have a rebuttal to. However, in the game's ending cutscene, Bowser tells his son that Peach is not his mother, which Jr. admits to having known all along.

The true identity of Bowser Jr.'s mother has not been revealed, prompting widespread speculation among fans.

Solution?
In a promotional video for Super Mario Maker and the 30th anniversary of Super Mario Bros., "Mario Myths with Mr Miyamoto", series creator Shigeru Miyamoto answers questions about Mario lore.

When asked about this mystery, Miyamoto nods before pointing to himself, suggesting that he is the mother.

This was (probably) a joke about Miyamoto creating Bowser Jr. as a character. Miyamoto otherwise appears to identify as male, and he has not yet had any physical role as a character in the Mario franchise.

Princess Peach
Though Super Mario Sunshine claims that Princess Peach is not Bowser Jr.'s mother, fans have still speculated about the possibility. The fact that she never denies giving birth to Bowser Jr. is used as evidence that she may recall being his mother or causing his birth, in some way.

There is little else to suggest that she is his mother, and due to the aforementioned ending cutscene, this theory is essentially debunked from the start.

Clawdia Koopa
A widespread rumor concerns an issue of a United Kingdom Nintendo magazine referring to Bowser's wife as "Clawdia Koopa". Despite the rumor's popularity, no scan or direct quotation of the statement has surfaced.

The claim is widely attributed to "Nintendo Power UK", a publication that doesn't exist. None of the British Official Nintendo Magazine's name changes have been related to Nintendo Power.

The true source of Clawdia Koopa is most likely the Mario fansite [//lemmykoopa.com Lemmy's Land]. Its webmaster created a fan character named Clawdia to serve as Bowser's wife in fanfiction. He has claimed authorship of Clawdia [//web.archive.org/web/20020802141637/lemmykoopa.com/lkmain.html since 2002].

No one
Some have theorized that Bowser Jr. actually has no mother, as the world of the Mario series does not entirely reflect reality, and children may be produced asexually in its universe. Many other animals reproduce asexually in a similar fashion, so Bowser could potentially do so as well.

Super Mario World 2: Yoshi's Island confirms that babies in the Mario universe are brought to parents by the stork, and since Bowser himself only had Kamek as a parental figure in that game, it's entirely plausible that Bowser Jr. has no mother either. Baby Bowser also looks near identical to his future son, further supporting the theory of asexual reproduction.