Speaking of Master Levels, I haven't played them in years, so I don't remember most of them and how hard they were but I definitely remember that TEETH gave me a lot of trouble (fuck the ambush at the start of the level, that alone is the reason this map is so damn hard) and I remember last year I said I was going to play them sometime but I've got sidetracked into other things and I will eventually do them, along with replaying Ultimate Doom and Doom 2, this time starting each level from a pistol start because I feel like I want to do them again and want an extra challenge (and yes I will still do them in original DOS EXE). When that will happen, I don't know.
I haven't forgotten either about Final Doom, No Rest For The Living, SIGIL and the cool wads made by the community and so on.
As for recommending source ports, I have some recommendations and I know I sounded so far like I am sort of purist due to the fact I played last year Ultimate Doom and Doom 2 in DOSBox and will continue doing so. It is true, I prefer to play certain types of wads in certain source ports, at least since the last couple of years. The original Doom games (Ultimate Doom, Doom 2, Final Doom, Master Levels) as well as classic megawads such as Memento Mori 1 & 2, Icarus, Requiem and so on (mostly 90s wads), I prefer to play in original DOS exe for the intended experience. In some cases (such as 2000s and 2010s vanilla compatible projects, example: Doom The Way ID Did), I use either Chocolate Doom or Crispy Doom, so I don't have to worry about the original DOS exe limits, while the game retains the original Doom feeling. This includes being able to save the game in a large level without crashing the game (I don't have the patience of completing a long level without saving) and easily loading mods that required merging with iwad and other old weird methods of installing the mods by modifying exe and iwad, which I'm not a fan of. I don't like the game files being modified, so using a source port is a must for certain older wads that involved modifying the game files.
When comes to a much smoother experience for playing vanilla, limit-removing, Boom and MBF compatible wads, I recommend both Eternity Engine and PrBoom-Plus. Eternity is an advanced Doom source port that combines the original Doom compatibility with editing and gameplay enhancements (sort of a cross between vanilla and ZDoom, except without losing any of original Doom compatibility). It also supports Master Levels and No Rest For The Living as episodes for Doom 2 if you configure the path to them. When you select Master Levels, it will show you this menu and allow you to select any wad:
I think it is very handy, it allows you to play the levels without having to mess with the command line parameters or exit the game and start again. Of course you still have to pistol start the levels but I don't think it's that bad to be honest. The levels were originally meant to be played from pistol start and I think most Doomers can do the levels just fine.
I also find Eternity to be a very underrated port. I wish more people used it, especially for the recently released SIGIL which supports it as 5th episode in menu (Eternity has its own MAPINFO support, which supports more episodes in the menu). It even has nearly finished Heretic support (the next version should support it fully) and I'm sure Hexen and Strife will also be supported one day. It would be nice to have a non-zdoom source port that supports all the Doom engine games, that way people have a middle ground between vanilla and ZDoom, for the other Doom engine games. The only downside of Eternity Engine is that it has no compatibility levels (it has a compatibility menu for changing certain behaviors but most people wouldn't know what exactly to change in case of a problematic level) and some levels may not work correctly, for example UAC_DEAD.WAD (Doomsday of UAC). I remember years ago I played it on Eternity and got stuck, because it relied on old Tag 666 behavior that was working on old Doom versions, which was changed in Ultimate Doom. And since Eternity only emulates Ultimate Doom's behavior, you get stuck. Thankfully there is a solution below...
PrBoom-Plus is a very popular Doom source port that has very high accuracy with original Doom and can play pretty much any vanilla/limit-removing/boom/MBF wad, as long as you set the right compatibility level (usually the text file that comes with the wad specifies the right -complevel command) and it is extremely popular among Doom speedrunners. I was initially turned off by this port because of the default settings with the wrong aspect ratio with squished status bar but after messing with the settings and managing to make it look exactly like original Doom, the port just became one of my favorites. Much like Eternity, it runs pretty smooth. I highly recommend it and it is a lot more stable than Crispy Doom, IMO.
For the popular ZDoom and GZDoom ports, I only use them when playing a ZDoom/GZDoom wad or when the author of mod recommends it.
Anyway speaking of SIGIL, version 1.2 just got released:
https://www.romerogames.ie/si6il