After having played multiple versions, I can say that PS versions are the best, with smooth scrolling and player-friendly UI. The deal with the music is kinda the same as DDS2/KMT2 - the original sounds better, but remixed tracks are also fine. Vanilla version of PS SMT2 was full of bugs, so be sure to get the revised version with golden PRESS ANY BUTTON text at the title screen (the revised version was uploaded here not that long ago). PS version of SMTIf has LOTS of new content and small fixes, including new awesome music in Akira's route.
GBA versions are okay (great UI, new content), but the music quality and scrolling sucks.
iOS versions of SMT1&2 were ported from GBA (featuring Visionary Items), but use PS music, with added extended versions of tracks from SMTIf. iOS version of SMTIf is a port of PS version (with smooth scrolling).
PCE CD version of SMT1 is okay, but the scrolling feels choppy. It also doesn't have that much unique content - only 4 new demons and while some animated cutscenes look great, the others are epilepsy-inducing. The music sounds different, because it's in FM, but it's pretty cool.
Mega CD version of SMT1 is slow as shit (even with Quick Scrolling), but it has lots of unique content, ilncluding: 1. new kickass intro cutscene, 2. new demon spritework based on Kaneko's official artwork (Douman, Yakshini, etc), 3. new demons. The encounter rate is RIDICULOUS, even compared to the original SFC version. The final dungeon has different floors compared to the other versions. The remixed music is hit or miss; most of the tracks made in FM sound great though. There is also an alternate theme playing in the Mansion of Heresy.
There also was SMTif: Hazama's Chapter for mobile phones, which had lots of new content, similar to GBA versions, but good luck with finding it.
tl;dr:
>SMT1
PS -> iOS -> GBA -> SFC -> MCD -> PCE
>SMT2
Bug fix PS -> iOS -> GBA -> SFC -> vanilla PS
>SMTIf
PS/iOS -> Hazama's Chapter (Mobile) -> SFC