i havent played mk pc games for ages but here are some stuff i remember:
mk1:
there are at least 3 versions of the game. 2 dos versions where the first one is something like a beta and the second is like r3.0. playing like r.30, few stuff dont work like sub-zero's frozen fatality, cage dont have 2 heads, raiden's HK does about uppercut damage (wtf?). the nut punch had the famious "oh ball" voice lol. most cpu starts from 3.0 work in that pc version too. there was sound glitch which i dont remember excactly - it was something like getting flawless victory on a courtyard and the monks apploud you, the announcer's voice is fucked up and there are no voices until you get another speach move like scorpion's move for example. there was a patch that fixed that but it was for sb16 only. if you beat the 3rd endurance by time goro will not fall and the game will freeze. the third version is the one from the cd pack which i have played only once and have to check it again, its somewhere on cds. it was with a lot better sounds but the gameplay was still like r3.0 i believe. male ninjas jks are different.
mk2:
it was a mix from some previous versions and the last arc version. you have that corner elbow trap where if you trap someone in corner you can elbow them to death (aka umk3 runjab inf), you can even beat kintaro with this trick starting it from mid-screen lol. the dip switches menu for the dos version exists and its still unknown what the dip switches do (although there are tons of sites which say that dip switches are for fats, blood and etc). AICULEDSSUL is fucked up on a faster computers because you have completely no time to type it at the first screen, there was some trick with the pause i believe where you pause the game at the beginning to type the code and then unpause it before the last letter "L". the dead pool fatality is different than in arcade it was f,f,f,uppercut or block (i have to check it because i dont remember it lol). rh infs, and glitch cancels work. if you are shang and play vs scorp, after finish him morph into scorp and do his toasty fatality and your head will be in yellow/orange color. there is another version of mk2 which is on 1 cd with the mk1 version, i havent played this version yet but i have it somewhere, i will check if there are some other differences.
mk3:
the dos version is probably the best home version. it has everything that mk3 arc does + you get the end musics no matter if you do a fatality or not. nothing else to said i dont remember any exclusive gameplay differences there. the only thing is that there are no those weird "arrow" sprites in the mk3 dos version if i remember correctly. the win version is 1:1 like the psx version, even the codes are the same. you have different "select your fighter" music and the loading times. a lot of sound glitches.
mk4:
its the fastest mk4 home version. you got buggy endings and bios and midway was forced to release a special patch that fixed that. the floor in the arenas is horrible (not flat like in psx/n64). ugly shadows and missing parts from the arenas (like the other two ports). reptile's lair is like the one in the arcade (n64 had different variation of that stage). you have a little more juggle time after hits like jumphk for example. sometimes when you are fighting vs goro and you spam moves like sonya's flip kick the music dissappear. noob has different fatalities in all home versions.
there are probably a lot of stuff which i forgot, but this is what i remember, its been long time since i played this games.