There are some WADs out there that are just plain unfriendly. Sometimes there are console variables that need to be set, sometimes it'll only work in a specific game mode, sometimes the WAD is split into about fifty different files to cover for every single permutation of settings. This guide should help you make your wad somewhat less of a pain for the user to run.
Not everybody's going to know how to play with your mod. Heck, one person once complained to me that ammo limits were too strict in WW-Diaz (turns out, they had not set a Reload key and thought that the player literally only started with 12 pistol rounds!). The best thing you can do is include an instruction manual with your mod. Not a huge, fifty-page tome that describes the backstory and every little bit of lore - a simple, easy-to-reference instruction sheet that tells the user precisely, in as clear and simple terms as possible, what you need to do to get the game started and play with the game.
There are some mods out there, though, that really need the aforementioned tomes (All-Out War 2, for example). That's because the mods really are complex enough to need multiple pages of instructions. For your average gun replacement mod, though, all you should really need is a quick guide on what each weapon does and possibly a note that tells players to make sure to bind a reload key.
2. Clear up your filenames!
If they're anything like me, most Doom players will just have a folder full of WAD files. If your project comes with more than one WAD file - or even more than one readme file - make sure it's named similarly to the WAD file so that it doesn't get lost! The worst thing you can do to a player that just dumps files into one folder is to name your files something generic, like "doomtk.wad" or "readme.txt". Unless you plan on running your WAD file in DOS with vanilla Doom (or uploading your WAD to /idgames...Lord only knows why they still need you to do this), you don't necessarily need to limit your filenames to the DOS-standard 8.3 filename formats. Not to say that all WAD files should be called "HURDY-SPLURBY BORK BORK BORK.wad" - just whatever clears up the wad's identity at a quick glance.
3. Don't waste space!
In the majority of cases, WAD files don't tend to be very large, but I'm seeing some people complain about how some files are just too large. Well, you'd hate to throw out all that work to keep sizes down, so here's some tips on saving space...
Compression! Not just sticking your WAD file inside of a ZIP - look over the insides of your WAD file. Skulltag supports graphics compressed in PNG format (lossless, meaning the graphics will not be degraded in quality) and sounds compressed in Ogg Vorbis (in most cases, using the basic quality settings on OggEnc will result in a sound that is one-quarter the size of the original wave file with no loss of sound quality). With mods that have a lot of such files in them, this can really help keep sizes more manageable. (The current version of Agent Hernandez: Dawn of Tomorrow holds over 4,000 lumps worth of data and comes to just under 18 MB in its WAD form. If uncompressed, I'd imagine it being somewhere closer to 45 MB.)
Trim useless things! I'm amazed that this tends to be the case at times, but I've seen a few WAD files that have several sprites or sounds that all have the same name - indicating, in most cases, that a lump was "replaced" at some point during development. Delete the old files if you're going to put in replacements.
Re-assess the needs of the WAD file. If all you're making is a simple gun replacement, then you really don't need that 12-minute-long metal epic as the title screen music. Indeed, unnecessary MP3/OGG music tends to be the main contributor to most overbloated WAD files.
4. Tell me what things are!
If you really need your mod to include several WAD files, mention in the instruction manual (you did read point #1 about that, didn't you?) which WAD files do what, and preferably which order to load them in. So if you have the smoke and shell casing effects in another wad file, don't just leave your mod as "MyMod1.wad" and "MyMod2.wad" - either name them properly (point #2) or say which WADs are optional in the instruction card (point #1).
5. Don't make the user dive into the WAD file to figure out which map they're supposed to start on!
This one's a particularly sore subject with me. WADs occasionally do not include instructions or helpful MAPINFO lumps that tell me which map to start on. Some mods tend to name their maps in some really crazy conventions (All-Out War 2, ZDoom Wars, among many, many others) and I end up having to dig through the WAD file to figure out what all the map names are. Don't put your players through this. Once again, instructions!
6. ZIP woes.
Okay, so Skulltag supports loading compressed ZIPs instead of WADs now. When you're distributing such a mod, don't just upload the ZIP file! A lot of people tend to be confused when they open the ZIP file and see a bunch of Sounds, Graphics, Sprites, Music, and Actors folders. If you choose to use ZIP format for your mod, rename it to something that people are less likely to mistake for a ZIP file (PK3 seems to be a popular choice but anything works), then compress THAT into a ZIP file. Okay, so redundant compression will actually increase the file size slightly, but it's all in the name of user-friendliness, plus you can also include the necessary instructions alongside the PK3 instead of burying it in the PK3 itself!
That should be it for this list. Basically, don't assume that your player knows as much about the mod as you do. Throw 'em a bone at some point.