there are also the following spacecrafts:
Project Mercury by BigMac - you need to get the original mercury manuals and checklists to understand how to operate it
Soyuz mode by Diogom ... still in earlier stages of development but at least he provided the community with the 1st realistic Soyuz model with systems/cockpit
the Vostok with Gagarin (but not sure if it works in orbiter 2016....)
unfortunately, there is no real simulated Gemini out there, ... and this end all real spacecrafts I am aware of.
anyway, just to make sure you know, in Reentry (payware) there is a real Gemini (as well as a Mercury and Apollo) but i can't tell more, as i cannot run it on my pc so don't know about the fidelity of the simulations;
in FlightGear there is the Space Shuttle of Torster/Gingin which is super detailed, but again cannot judge the fidelity of the simulation in terms of orbital mechanics as cannot run it on my pc, but it is free.
of course there are many fictional spacecrafts, and real ones (current technology say) but without internal cockpits, systems and so on .... just orbiter style flying controls so to speak.
but i guess, considering that developers out there are managing to program real spacecrafts of the 1960s-1980s only now, almost 40-60 years later, when a lot of technical documents are now finally freely available in internet to study, i am afraid that similar level of details as Mercury, Gemini, Apollo, Space Shuttle, Vostok and one day Soyuz (hopefully) for contemporary spacecrafts will need to wait our sons / daughters before to be flyable on a tabletop simulator, even considering that all of them are built by private companies, so i guess that there will not be free technical operational and system manuals freely floating around to allow programmers to study and find inspiration to create their models .... as it seems we are now entering in a new era of private space race with so many new spacecrafts to be developed....sadly "life is too short"

to see and witness all these interesting developments (i wished to have been born only 20-30 years ago as most of you i guess

).