Sorry for the long delay in replying, I needed time to go back through my notes/copies and compose a response. Here is what I have found:
1) There were 2 Thomas Barnes, one in Farmington and one in Middletown.
2) Thomas Barnes of Farmington made a will date 9 Jan 1688 in which he mentions his wife Mary, sons Thomas and Ebenezer and other children. This will was witnessed by John Stanley and John Hooker, and probated 7 Feb 1689 (nfo from NEHGS, Early CT Probate Records) . There is also record of a marriage contract made between him and John Andrews on March 23, 1662/3 in which he states his intention to marry Andrews' daughter. Along with other conditions in this contract, he agrees to "put out" his remaining children, except possibly Benjamin and Hannah. (The American Genealogist, volume 9, also from NEHGS website). I didn't find any baptismal records for his children, but I have not done research on this family in a while.
3) Thomas Barnes of Middletown made a will dated 25 Feb 1683/84 in which he mentions his wife (not named), sons John, Thomas, Daniel, daughters Mercy Jacobs, Martha, Elizabeth, Abigail and a son Maibee. This will was witnessed by Daniel Harris Jr and John Hall Sr. and probated 7 Sep 1693 (NEHGS, Early CT Probate Records). There are records of baptisms in the New Haven Church of children of Mary and Thomas Barnes, in particular Maibee b. 25 Jun 1663 and bapt. 20 Jul 1663. Also, "Families of Ancient New Haven" p.90 lists Elizabeth, daughter of Thomas and Mary Barnes (widow of Benjamin Brockett) as b. 28 May 1650 and bap. Winter 1695.
4) Some genealogists list Mary Brockett as the Mary Barnes of Farmington who was hanged for witchcraft, and attribute the list of children in the Tom Barnes of Middletown will (John, Thomas, Daniel, Mercy, Martha, Eliz., Abigail, Maibe) to the Mary who was hanged, but I believe that is not the case. I did find a reference to a Lisa Johnson, Dir. of the Stanley-Whitman House in Farmington, who gave a presentation about Mary Barnes at the Bristol Historical Society back in 2006. From the article, it appears that she is dealing with a Mary Barnes of Farmington, the one whose husband made a marriage contract shortly after her death. Ms. Johnson mentions Mary Barnes' hanging on 25 Jan 1663, well before our Maibe/Maybee Barnes' birth.
Hope this helps, and that you can flesh it out more!