One of my favorite sleeper hits for the NES, The Guardian Legend, would have been awesome on the Turbo; less (or no!) slowdown, bigger color pallete... would've been gorgeous.
Another NES game that would have been great on the turbo is River City Ransom (or whatever the Famicom version is called - Kunio something.)
It's been said before, but I'll say it again: the Turbo needed more beat-em-ups.
Had Hudson/NEC bothered to do a real RPG on HuCard, they could have gotten Miracle Warriors from the SMS. Only 256k - I think it could easily have fit onto a card with gfx improvements.
moving on to 16bit ports, I think the PCE could have done Faceball 2000 as well or better than the SNES did, being a faster machine and all. FB2k, IIRC, has (one of?) the lowest color counts for a SNES game ever, and it isn't an FX game. Not that Faceball 2000 is a great game, but it would have proven that the PCE could do 3D.
And I realize it's an impossible dream, and some here will call me a snerd for saying it, but Secret of Mana on SCD(or ACD!) would have been awesome.
and speaking of the impossible, a Phantasy Star collection on SCD would have been wonderful - would have gotten some needed cash in Sega of Japan's pocket, and probably wouldn't have affected american genny sales at all. I often wonder why they didn't do this with the Sega ports they did get.