Dangerous Mods
Now that I got your attention, hopefully there aren't any dangerous mods on this site, but there are definitely some mods you should avoid and some instructions which are just plain stupid - as are the modders who created them. More reasons to backup!
Mods installed in games folder
Older mods, particularly those circa 2016, often instruct the user to install in the games folder. That's because mods folders weren't as common then or the creators just didn't care. Always install in your mods folder. If you mistakenly don't and have an issue, a verify integrity should fix the problem.
Mods which include dlclist.xml
Some mods will package a plain vanilla dlclist.xml file, which might date back to 2016, with just their mod added and instructions to replace yours with theirs. This means overwriting any and all addons you've added since you started modding. Don't install a mod's dlclist.xml. Instead, edit your own file.
Mods which include gameconfig.xml
Similar to mods which contain dlclist.xml, this one is even worse - mods which have their own version of gameconfig.xml, some dating back once more to 2016. This is likely a recipe for an instant game crash - particularly and ironically if your game is properly updated because you can't use an old gameconfig with a new updated game. Never install an old gameconfig.xml. Worst case reinstall a current one from this site.
Beware - the OIV Automatic Installers
The OIV method of installing is wonderful for anyone new and/or lazy. It does everything for you and will not make any installation mistakes if properly written and tested. Unfortunately, you don't know what the mod is doing. Some of them will overwrite files you have already modified. Others will replace your gameconfig.xml and/or your dlclist.xml as described above.
So don't use automatic installers unless you know for sure they are safe. An OIV is essentially an archive, so you can unzip them. Inside you will find a file called assembly.xml which will tell you exactly what goes where. You will also see a content folder that includes all the files that will be installed. If you want you can install the mod manually yourself by considering the assembly.xml file as your instructions.
If you don't feel comfortable doing a manual install, at least look at the content folder and if you see gameconfig and dlclist in there, backup your own files and then restore them (overwrite the mod ones) after the installation. Same logic applies for any other files where you want to keep your own versions but you see the mod might overwrite them by looking at the contents folder or assembly.xml.
Visual Mods/ENBs
These mods are very complex, installing and replacing dozens of existing game files or even files you have modified. As a result they are often problematic and are very difficult to uninstall. If you're the type of person who prefers the unnatural looking visuals, at least backup your files before installing these.
Malicious Mods. Exercise caution if a mod is only available as an executable, for example those that end in in .exe or .bat, like setup.exe. There have been a few cases of mods containing viruses. One with the legitimate version of QuantV and one with a spoofed SHVDN, both in 2022. To protect yourself only download from official sites, backup your files, and use an anti-virus software (although these are not foolproof). OIVs can also contain harmful code but they can easily be opened and inspected. Finally even .dll files can contain harmful code.