This OP may be updated over time, and new posts will be made to point out any significant additions.
For those who experience the issues, please walk though these suggestions and make a post with your responses.
To download the newest EDuke32 / VoidSW builds: https://dukeworld.duke4.net/eduke32/synthesis/
To download the newest NBlood / Rednukem / PCExhumed builds: https://lerppu.net/wannabethesis/
EDuke32 has received fixes since release of Ion Fury v1.02. For testing purposes, please copy eduke32.exe r8494 or later to "%APPDATA%\Ion Fury" and use it for testing instead of the provided fury.exe.
Basic Information
Describe the symptoms you experience. How often and in what circumstances do they occur?
What are your system specs? OS, CPU, GPU, RAM, Disk, Display.
What display settings are you using? Resolution, Bit Depth/Renderer, Refresh Rate, Windowed/Fullscreen.
Most people reporting these issues only get them with the EDuke32 family of ports and have no issue with other games, so it's probably not a matter of simple user error. For completeness we'll list common things to verify here but you may be able to skip to Diagnostic Questions.
Diagnostic Questions
What FPS limiter settings are you using?
If using NVIDIA, does enabling Threaded Optimization in the driver control panel help any?
Does turning off both Sound and Music help any?
Open the console ([~] in EDuke32/NBlood/etc, [Shift]+[~] in Ion Fury) and try the following cvars: r_glfinish, sys_timer, win_systemtimermode, win_priorityclass. Typing them in by themselves will show the options that are available. Follow them with a number to change their settings. Run the "restartvid" command after changing any of these options to make sure they apply. Do you notice any difference?
[Optional, Advanced] Some CPUs from 2017 onward may have a performance issue with their implementation of the High Performance Event Timer. Try switching Windows' QueryPerformanceCounter from HPET to TSC using the instructions at this link to see if there is any benefit.
If you wish to use VSync:
Is there any difference between turning VSync on in-game, and turning it off in-game and enabling it in your graphics driver's control panel instead?
Does the FPS Offset option in Options > Display Setup > Video Mode help any? Start with -1 and +1.
Is your system capable of GSync or FreeSync? Is it enabled? The preferred way to enable GSync is to enable VSync system wide in the NVIDIA Control Panel (set to On, not to Fast Sync), disable any VSync options in the game, and tweak the FPS Offset option to your satisfaction. Some older GSync monitors may benefit from an FPS Offset around -3.
Does enabling Triple Buffering help at all? If so, does input lag increase?
Open the console (explained above) and try different values for the r_vsync cvar. (Before r8612: r_swapinterval, r_swapcomplete) Run the "restartvid" command after changing it.