So, the Monogatari series has four season, and soon will be five, and if we look at the production order, based on this question, and this Wikipedia page it will be:
As you can see, "Second Season" is the fourth and fifth season of anime, so why the title "Second Season"?
The word Second in the anime title Monogatari Series: Second Season is not based on the number of times the series has been animated (which is the usual practice), but rather based on the fact that the anime adapts the content from the Second Season of the Monogatari Series, which consists of 6 volumes (listed in order of publication): Nekomonogatari (White), Kabukimonogatari, Hanamonogatari, Otorimonogatari, Onimonogatari, and Koimonogatari.
The anime Monogatari Series: Second Season (summer 2013) has adapted (listed in airing order) Nekomonogatari (White), Kabukimonogatari, Otorimonogatari, Onimonogatari, Koimonogatari. And this summer (2014), Hanamonogatari will be animated under the title Monogatari Series: Second Season Hanamonogatari.
The term Second Season has been in used since mid 2011 in Monogatari Series article on Wikipedia.
It also has been used on an anime news site in March 2011, regarding the release of Hanamonogatari (emphasis mine).
第変話「するがデビル」を収録した西尾維新『花物語』の発売日が3月29日に決まった。『花物語』は化物語シリーズ セカンドシーズン『猫物語(白)』『傾物語』に次ぐ第3弾。
As for why the 6 volumes are collectively called Second Season, according to Wikipedia article of Monogatari Series in Japanese:
『猫物語（黒）』で当初の予定であった暦とその周辺の人物の物語は一通り終了したが、『化物語』のアニメ化に触発されて「セカンドシーズン」が発表された。
My own translation1:
1 Feel free to edit in a correct translation.
Although the series was initially planned to end at Nekomonogatari (White), at which point the series have finished telling the story about Koyomi and all the people around him, Nishio Ishin was inspired by the anime adaptation of Bakemonogatari and announced the "Second Season".
The old version of the article noted the date of the announcement being June 2010.
Then, Bakemonogatari (2 volumes), Kizumonogatari, Nisemonogatari (2 volumes), Nekomonogatari (Black) are collectively called First Season for the sake of convenience after the Second Season was announced.
セカンドシーズン発表後に便宜上「ファーストシーズン」と呼ばれるようになった。
Unfortunately, the article (old or new) didn't cite any source regarding the announcement of the Second Season of the novel.
I'll take a shot at this. The Bakemonogatari wiki groups the Bakemonogatari volumes, the Nisemonogatari volumes, Kizumonogatari, and Nekomonogatari Black together as Season 1. The stories adapted in the Second Season anime, plus Suruga Devil, are grouped as Season 2, and the rest are Season 3. Wikipedia corroborates this. So it is based on the novels, as nhahtdh says. And of course, since the second season anime covers five different novels (Neko White, Kabukimonogatari, Otorimonogatari, Onimonogatari, and Koimonogatari), they couldn't just reuse the name of the novel like with the Bake and Nise anime series.
As to why the novels are grouped like this, it's hard to say, so I'll speculate wildly. First of all, notice that if the Monogatari series had used a regular season (26 episodes) for the anime, instead of short seasons plus ONAs, that would just about cover Bake (15 episodes) and Nise (11 episodes), and then we'd have a four-episode Neko Black OVA and possibly a Kizu movie, if it ever got made in this alternate reality. It's possible that Nisio Isin recognized this when he decided to assign those novels to the first season. Also note that the second season did fit fairly neatly into one 26-episode season, which could have contained Hanamonogatari if they'd cut out all the review episodes.
Second, look at the content of the stories. Bake and Nise together cover a single story for each heroine, including Karen and Tsukihi. The other two first-season entries, Kizu and Neko Black, are prequels, and Kizu is sort of the first Shinobu story. The second season novels all take place after the first season novels, and give a second story for each heroine, narrated by that heroine in many cases, with the exceptions of Kabuki-, Oni-, and Koimonogatari. The second season stories are also tied together by the presence of Ougi.
I have no exposure to the third season novels, so I can't say how they fit in. But it does make some sense that the novels would be grouped like this, even though the anime adaptations didn't carry this grouping over with the first season novels.
