I think most Falcom games can be more appropriately labeled remakes than ports. The differences in Dinosaur Resurrection veritably render the original obsolete.
Other than Falcom games, the only ones that come immediately to mind would be a Dragon Knight IV remake from (I think) 2007, and Ryuuki Denshou: Dragoon, which was remade for Windows 95 (I believe "Plus" was appended to the title), and that version was then ported to Playstation.
. . . and that just gave me an idea for another request.
Oh, and I think some of the Farland Stories may have gotten ports.
also also, I haven't verified this, so don't know any titles, but I was told that some Chinese and Korean games made for windows were ported to PC98 for their Japanese release.