If anyone wants to run this topic instead of me or wants to use the information here I see no problem with that, just hope it's ok with everyone who contributed.
My general thoughts regarding the structure of this thread.
The way I see this topic is that it should be as short as possible since I think having a wall of text will discourage many users from actually reading it. Basically I want to make new users aware of the different aspects without to much detail. It would be up to the user to search for additional information on the topic. I have been considering that I could provide additional information with spoiler tags and still keep it short. Feel free to add any other tips or guidelines that you feel belong on this list. Ps: English Isn't my first language so if anyone wants to rewrite anything so that it's easier to read then please do and I'll update the text /smile.png' class='bbc_emoticon' alt=':smile:' />.
---This is a work in progress, everything in this post might not be 100% accurate!---
General advice
Install the game outside of the Program files (x86) folder.
On windows 7 and Vista Steam installs the game under c:\Program Files (x86)\Steam\SteamApps\Common\Skyrim by default. Having the game installed to this folder can cause issues with a lot of mods.
Create backups before adding/removing/updating mods.
Incase something goes wrong you can restore the backup, that way you don't have to reinstall everything.
Only install a few mods at a time.
Not all mods work together and if there are any bugs or your game crashes it's easier to find the mods that cause them. It's often a combination of mods that cause these issues and not the mods on their own.
Be careful when installing older mods.
Mods made before the creation kit was released can cause stability issues if they have not been updated.
It is generally advised to never use anything older than February 7, 2012.
Make sure you have a proper load order.
If you use mods that have .esm or .esp files then it's important that your mods are loaded in the proper order.
Savegames
Never overwrite a save game.
[FALSE]
The game doesn't overwrite a savgame but instead replaces it with a new one so "overwriting" a save is the same as creating a new one.
Don't use auto saves or quick saves.
[FALSE]
The game handles auto saves and quick saves the same way it handles saves done through the menu. Therefore they are no different than regular saves and point 1 also applies here.
If you die restart the game before loading a save game.
[UNKNOWN]
In general this shouldn't be an issue but there have been reports that some mods require a restart of the game.
Restart the game before switching to another character.
[TRUE]
In some cases data gets carried over when you swap to another character so the safest thing to do is to restart the game (quit to desktop) before doing so.
Updating or uninstalling a mod might corrupt all subsequent savegames, leading to crashes, poor performance and excessive savegame size.
[TRUE]
Updating or uninstalling a mod which uses Skyrim's scripting system will cause no issues if the mod writer has coded it correctly. However, it is possible for a perfectly working mod to have accidental coding errors which might cause irretrievable savegame corruption if it is uninstalled or updated. Some mods, by their very nature, will be more likely to have these errors than others. As a general rule of thumb, updating mods without uninstalling them is safer, but still not guaranteed safe. Exercise caution, and always be prepared to revert to a save made before the mod was ever installed.
Optimizers
Programs that optimize textures can cause crashes if used in conjunction with certain mods.
[FALSE]
Optimizing textures can degrade their visual quality and by doing so increase game performance but it's considered safe to do so.
Programs that optimize meshes can cause crashes if used in conjunction with certain mods.
[TRUE]
I't's not recomened that you do this currently.
Leftover topics
I was planning on writing about these aswell but I don't have enough free time to do it right now. If anyone wants to write any of them then please do and I'll add it to the list.
Installing textures VS what your system can actually handle and how to monitor it.
Using steams default behavior of backing up your saves to the cloud.
How to minimize the amount of programs running in the background.
Mod managers.
Help maintaining a proper load order.
Cleaning mods.
Bloat.
Unofficial patches.