Smalltalk was developed on in-house custom hardware (the Xerox Alto) at Xerox PARC.
Java was developed on Unix at Sun, presumably on SPARC hardware.
C++ was developed on Unix at AT&T. No idea what hardware but probably VAX or AT&T 3Bx.
R started out life on Unix, but has been ported further afield.
Python was developed for Amoeba (a research O/S) originally
LISP was developed on early IBM hardware (I think an IBM 704?)
FORTRAN was developed on early IBM hardware.
Unix as a platform was and is very hackable. Basically, unix was originally designed first and foremost to be a programming environment and it's quite easy to program for.
That is one of the reasons Computer Science departments like it. Of the list above, C, C++, Java, Perl, PHP, MATLAB, R and (IIRC) Ruby originated on Unix. The same can also be said of Tcl/Tk. Amoeba had fairly unix-like API's and Python was ported to unix fairly early on in the piece.
LISP and Fortran both started on IBM mainframe hardware of the era - late 1950's. There was quite a bit of activity on these machines as they were the incumbent architecture of the day. However, the field was much more rarified at that point as there were fewer installed computer systems and fewer people with access to them.
The heyday of Unix in the 1980s and 1990s was a sort of window when many people had access to powerful computer equipment that they could hack on but the industry was still growing and had not consolodiated to the point that the tyranny of the masses started working against the sort of forces that permitted this sort of innovation. For such a large installed base, Windows has contributed far fewer widely accepted programming languages, although some of them (e.g. VB, C#) have a large user base.
Windows is quite a difficult platform to code for at a system level and early attempts at frameworks such as MFC still have a somewhat deserved 'here there be dragons' reputation. Even VB6 had a lot of leaky abstractions and coding a complex application in it is not all that easy. .Net has taken care of most of the leaky abstractions and is quite a pleasant system to work with - especially compared to VB6. Most of the innovation in languages on Windows these days is happening against the CLR.