In "Introduction to the Tiberian Masorah", I. Yeivin dedicates a section on the order of the books. Here is a summary:
The order of the Torah and early Prophets was standardized in antiquity. The order of the later Prophets and Writings varies in the literary sources.
TB Baba Batra 14b gives the order
ת"ר, סדרן של נביאים: יהושע ושופטים, שמואל ומלכים, ירמיה ויחזקאל, ישעיה ושנים עשר... סידרן של כתובים: רות וספר תהלים, ואיוב ומשלי, קהלת, שיר השירים וקינות, דניאל ומגילת אסתר, עזרא ודברי הימים.
Joshua, Judges, Samuel, Kings, Jeremiah, Ezekiel, Isaiah and the Twelve... The order of the writings is Ruth, Psalms, Job, Proverbs, Qohelet, Sons of Songs, Lamentations, Daniel, Esther, Ezra and Chronicles.
The late Prophets are sometimes ordered like this in (usually Ashkenazi) manuscripts. Masoretic, Sephardi and Italian manuscripts follow the order of today with Isaiah before Jeremiah.
Sefer Ha-Hillufim gives this as the Babylonian order. The order found in Tiberian Masoretic works (Aleppo codex, Leningrad Codex, MS Sassoon 1053, etc.) is the order that Sefer Ha-Hillufim calls the order of Eretz Israel:
Chronicles, Psalms, Job, Proverbs, Rush, Song of Songs, Qohelet,
Lamentations, Esther, Daniel, Ezra
The order followed today is seen in Ashkenazi MSS, with Chronicles at the end of Writings, Proverbs before Job and the Five Scrolls in the order they are read in the year from Nissan (Song of Songs, Ruth, Lamentations, Ecclesiastes, Esther).
In Masoretic MSS, Samuelm, Kings, Chronicles and Ezra-Nehemiah are considered as single books. Psalms is divided into 5 "scrolls."