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When was the current pagination of the Gemara finalized? It seems that it was before the Vilna print, though it seems from different Acharonim (the Rama, etc.) quoting the Mordechai that the Mordechai used to be referred by page number.

Also, was any other Rishon ever printed on the side of the Gemara instead of Tosfos?

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@Vram AFAIK, most of the old Maarei Mkomos to the Mordechai went by page number. – Shmuel Brin Feb 23 '12 at 4:34
up vote 11 down vote accepted

The standard pagination and layout of the Gemara follows that of Daniel Bomberg's edition of 1520-22, which was the first time that Shas was printed as a complete set. (Earlier Jewish printers, including the famous Soncino family, had produced only individual volumes.) A notable difference is that Berachos has 66 pages as compared to today's 64; that change was made in his next edition, approximately 1526-39.

There have been editions where Tosafos (and even Rashi) were omitted, but it doesn't look like there have been any where they were replaced by other commentaries. See Marvin J. Heller, "Earliest Printings of the Talmud," and Edward Fram, "In the Margins of the Text."

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