PLEASE NOTE: THESE BUG FIXES WILL NOT WORK FOR EVERYONE. THEY SHOULD WORK FOR THE MAJORITY HOWEVER.
If you have tried all the steps mentioned, please post with the specific issue and ALL steps you have done, as well as your PC specs wrapped in a spoiler tag.
Here are a few off the top of my head, and I will keep this list up to date as much as possible:
Red Logo/Loading Screens
Check your Skyrim Data folder (steam/common/skyrim/data) and look for a 'fishy' ini file. It may be the name of a mod you have (killable_children_1_0_1.INI, Tytanis.INI, realisticwater.INI, etc etc.), or it may be skyrim.INI. I don't know about other users, but I personally noticed the all-cap INI ending, and moved it out of the folder. This fixed my Red Logo, as well as fixed other users Red Logo's.
Probable Cause:
Saving ini file in console command within Skyrim
Solution:
Remove (DO NOT DELETE) any strange ini file from the Skyrim DATA folder. Once you confirm the Red Logo is back to silver, it is safe to delete the ini file you moved.
Bugged Radiant Quests
While exploring, you can (and often will) come across a quest item for a quest you've never received. Once you find the quest start, the quest becomes 'bugged' and it appears that you are unable to complete it. Using console commands, you can force drop the quest item and reclaim it to continue.
To find the ID of the item in question, head on over to http://www.uesp.net/wiki/Main_Page and search for your item. Then open up the console and type the following command:
player.removeitemThe quantity should always be 1, but there may be exceptions.
You can also try exiting the quest-givers area (fast travel somewhere, fast travel back) and reattempt to talk to the NPC with the quest item. This personally worked for me.
Game Time Unsynched
Taken directly from this thread http://www.gamesas.com/index.php?/topic/1291005-bug-game-day-not-in-sync-with-game-time/:
Skyrim's game day cycle is NOT properly synchronized with the game's clock, with days changing at seemingly random times instead of 12:00 AM when it is supposed to. If this continues for extended periods, it can result in a seriously broken clock, which can have disastrous effects on the game's AI. Specifically, any packages that are tasked to be executed on a certain day will become broken because the game day is cycling at... say, two in the afternoon. The cause of this bug is currently unknown, but what is known is that it NEEDS to be fixed, as it IS game-breaking.
There have also been sporadic reports from PS3 users saying this has happened to them, too, though I cannot confirm it for them. If that is the case, the problem might be that the game day cycle is frame-timed (though I can't say for sure what the problem is).
Workaround: if you notice your game clock has fallen out of sync with the game day, wait until precisely the moment the day changes, the type "set gamehour to 0" in the console. This will temporarily fix the clock.
There have also been sporadic reports from PS3 users saying this has happened to them, too, though I cannot confirm it for them. If that is the case, the problem might be that the game day cycle is frame-timed (though I can't say for sure what the problem is).
Workaround: if you notice your game clock has fallen out of sync with the game day, wait until precisely the moment the day changes, the type "set gamehour to 0" in the console. This will temporarily fix the clock.
Shadow Artifacts
Some people may have noticed that their shadows are completely bonkers in Breezehome after the 1.3 patch. I am referring to the rings of shadows that look absolutely horrid, and can actually hurt your eyes if you look at it too long. The 'simpliest' fix is to set iBlurDeferredShadowMask= to a value to like 5 or 7.
Alternative, there is an in-depth guide located http://www.hardocp.com/article/2011/11/23/tweaking_skyrim_image_quality/2 that showcase some hardcoe shadow modification in the ini files.
Stuck Spell Effects
Players sometimes get attacked by a Spriggan, and will find that the effect has 'stuck' to their player. This is also true with other various spells (Such as Ice Lance, Frost, Fire, etc etc). To fix this simply open up console and add the specific spell to yourself, then remove it. I have not personally experienced this bug, so I cannot comment from personal experience if it works or not.
player.addspellNote: If you already have the spell (Ice Lance, for example) You may have to remove it then readd it again. Again, I am not clear on how this process actually works, as I have not personally encountered it.
http://www.uesp.net/wiki/Skyrim:Spells
You open the console and type "help 0". Use quotes for spells with spaces. ("Chain Lightning") You can then use page up and page down to scroll through the list to find the spell code you want.
I modified the original quote for easier reading.
Headless Body Glitch
While using TIM and TGM, it is possible to be decapitated, yet you will not die. This results in a humorous glitch, that will ultimately crash the game after so long.
To fix this simply open up console and type:
sixchangesixchangeplayer.removeitem(I am still looking for the head stump code.)sixchangesixchange
No Spoken Dialogue
Quite simply, some NPC's become mute for some reason or another. You'll see the subtitles, but there is no spoken speech. To fix this, use a http://www.tesnexus.com/downloads/file.php?id=3117#content to unpack Skyrim - Voicesixtra.bsa
Random CTD's
There is not a 'confirmed' fix to this, but I have discovered a few 'stability' tricks that may or may not help. Each person's setup is different, so there is no way of knowing exactly.
First, you need to do a personal check list:
Have you installed any texture packs?
Have you tinkered with the ini files?
Do you have the necessary specs?
These are things that I have personally done to reduce the frequency of CTD's on my machine.
My specs/mods
Spoiler
Specs:
AMD Phenom II x4 955 @ 3.2ghz
AMD HD6950 2GB Graphics Card w/ 11.11b drivers
12GB DDR3 1600 RAM @ 9-9-9-24
1TB HDD w/ 64mb Cache
12GB Paging file
Mods:
SKSE with Container Organization and MEMDisplay (I forget the actual name, but it shows the mem usage in the upper right corner)
Realistic Water
Majoras Mask Moon (This is actually pretty funny)
ALL of xevius's (I don't know off hand if this is the correct spelling) body mods
Tytanis' Ultimate Mod
ENBSeries ANTICrash patch 0.09
Reduced LOD Noise (again, I forget the actual name, but it blends the terrain better between the loaded and unloaded cells)
ugrids @ 7
lots of other ini tweaks, pm me for the full list
Specs:
AMD Phenom II x4 955 @ 3.2ghz
AMD HD6950 2GB Graphics Card w/ 11.11b drivers
12GB DDR3 1600 RAM @ 9-9-9-24
1TB HDD w/ 64mb Cache
12GB Paging file
Mods:
SKSE with Container Organization and MEMDisplay (I forget the actual name, but it shows the mem usage in the upper right corner)
Realistic Water
Majoras Mask Moon (This is actually pretty funny)
ALL of xevius's (I don't know off hand if this is the correct spelling) body mods
Tytanis' Ultimate Mod
ENBSeries ANTICrash patch 0.09
Reduced LOD Noise (again, I forget the actual name, but it blends the terrain better between the loaded and unloaded cells)
ugrids @ 7
lots of other ini tweaks, pm me for the full list
I was using ugrids 9 and crashed usually every 5 minutes or so, depending on what I was doing. I reduced ugrids to 7, removed FXAA (and disabled it) injector, reduced some shadow settings in my ini file, as well as other various reductions in the ini files. If you wish to reduce your ini tweaks, but don't know where to begin, the best solution is to start from vanilla again by removing ALL .ini files from both Skyrim's Data folder as well as the ini files located in my documents/my games/skyrim, and re-verifying cache integrity via Steam, then slowly working up to the settings you had until it starts to crash again and scale it back a notch. If you have extremely similar specs as mine and wish to use the ini settings that I have personally found to be the most stable, PM me and I will send you the info.
If there are alternate bug fixes, post them here and I will update accordingly. If you know of other bugs and their fixes, post them as well and I will update this accordingly.
Good luck, we are all counting on you.
-Noodles.