As someone who owns a SD-90 (plus its smaller cousin the SD-20) and has a compatible MU module (namely the MU1000-EX), I'll give my two cents. (Also, if need be, I can provide a few recordings.)
I do not really recommend the SD-90 for use in DOS and Windows gaming. GS compatibility does exist, but the samples are taken from a mishmash of other Roland Sound Canvas modules that make it sound poor for compatibility. Its GS implementation also covers 226 patches (equivalent to a SC-50, AKA no CM-64 and MT-32 "emulation" banks from the SC-55) only. Not to mention the XGLite support on said module just exists, and I'd take any MU module over that any day.
However, the SD-90 does have its uses for some music production usage (though I'd honestly take any JV or XV module instead if that is your goal), and has a particular notoriety amongst Touhou Project fans for some of its instruments (particularly Romantic Tp.). Additionally, as a GM2 module or in native mode, I find it decent thanks to the ability to freely select between 4 different GM2 banks; in fact, I prefer playing Descent with this module after adjusting the drum bank.
As for the MU-50, from what I understand of it, it has full baseline XG support as well as some extra patches from the MU80, but loses out on some effects processing (generally not too important though for most uses). You will be able to use the TG300-B mode as well for a good degree of GS compatibility.
Regarding hooking either module up to your system for use in DOS and Windows alike, you can get a gameport-MIDI cable adapter, connect said cable to the joystick port on your sound card, hook the cable's MIDI Out to the module's MIDI In, and then set the module's mode to MIDI (done via hardware switch on the MU-50, System menu on the SD-90). Then for the audio, you can connect the sound card's headphone output to the inputs in either module (RCA in the SD-90, either RCA or 6.3mm on MU-50) and connect your master output device to the module's headphone or output jacks. Also in the case of the SD-90, you may need to adjust the Analog In setting to Line in the system menu, and maybe also bypass the default digital audio effects.
Both modules also support serial (MU-50) or USB (SD-90) connections under Win9x provided drivers, with the latter also acting as a USB sound device.
CM-64, FB-01, SC-55ST, SC-8850, SD-20