This guide after v469 Patch
Since the v469 patch has Raw Input the info on this page about DirectInput, Mouse Smoothing and the MarkC Mouse Fix is obsolete.
Mouse Tracking & Input
Arguably most of this page could be considered as placebo settings, but they are all the known settings to improve UT/TO mouse input and feeling.
Another important topic is the max fps / frameratelimit, you can read more on that on the bottom of this page.
Mouse DPI And Polling Rate
It is said that UT99 and TO do not handle a High Mouse DPI and Polling Rate very well. These days a modern "Gaming Mouse" can have maximum DPI levels up to 16000 DPI and a USB Polling Rate up to 2000.
Most suggest to use a dpi from 400 up to 800 and a maximum USB Polling Rate of 1000. But this is something you will have test and see what feels best for you.
If you don't know what these are i suggest to Google Search this topic. Most likely your Mouse will not have a higher USB Polling rate of 1000. If you don't know your Mouse DPI Setting try to find a button on your mouse that when you press it, it slows down the speed of the mouse cursor. Try to find the lowest setting and use that for playing TO.
Windows Mouse Settings
Make sure "Enhance pointer precision" is disabled and the "pointer speed" is set to setting 6/11 in the Windows Mouse Settings. This is always recommended no matter what game you play. It is a requirement if you want to use the MarkC Mouse fix and have DirectInput disabled in TO. (For example to fix the ALT+Tab Crosshair bug).
DirectInput and Mouse Smoothing
Most people play with DirectInput enabled. This gives decent mouse aim but gives the known ALT+TAB Crosshair bug, where alt tabbing multiple times can give a white or grey large crosshair on the middle of your screen. Some find this annoying, some use this to make it easier to snipe with the MSG as you now have a crosshair when not using the scope, making it easier to flick to a target before actually zooming.
Most also disable Mouse Smoothing since you don't want your mouse input to be smoothed. But this is a personal choice.
MarkC Mouse Fix
The MarkC Mouse fix is meant to fix the mouse input for older games that use legacy input methods. It is used by players who like to disable DirectInput because they ALT+TAB allot and because it supposedly should give a more 1:1 mouse input then using DirectInput.
Download: MarkC Mouse Fix
To install the MarkC Mouse Fix make sure to check the included readme. Basically you must open the Windows folder of the windows version you are running currently, and select the registry file with the DPI that you currently have in Windows. This is most likely 100% but check your Windows Display settings see to what the "Scale and Layout" Percentage is set to.
CPU Power Saving Features
Since the UT engine uses your CPU speed to time various things, it is supposedly bad to have your CPU change its frequency while playing. On default "Windows Power Settings" and default Bios Settings there is a chance your CPU might change frequency up/down depending on the load.
A simple way to fix this is to set the "Minimum Processor Frequency" to 100% in your "Windows Power Settings"
A advanced method is to disable all Power Saving Features in your Motherboard's Bios. Depending if you have an Intel or AMD Processor the names of those settings might change, only change the settings in your Bios if you know what you are changing so most likely YouTube or overclock.net can offer you instructions.
A theory from back in the day is that the game’s .exe process might get shuffled around to different cores by the Windows Scheduler and this can create small stutters or hitches.
Easy method but it has to be repeat every time you start the game
Manually ALT+TAB out of the game, open Windows Task Manager, click on TacticalOps.exe and set the CPU Affinity to Core 0.
Create Custom .bat starter
Open Notepad and paste the following
start /affinity 1 TacticalOps.exe
Save this as a .bat file in the System folder of your TO where also the TacticalOps.exe file is located, make sure to set "Save as type:" to "All Files (*.*)" or you might save it as Starter.bat.txt and then it won't work.
You can even create a shortcut of this .bat file, give it a custom icon from the "Help" folder and it looks like the original shortcut.
Convert Sensitivity From Other Games
If you don't keep track of your cm/360 (How much to move your mouse for a 360) you can convert the sensitivity of other games to UT/TO on mouse-sensitivity.com.