Global Flag Summary
Adds a way for you to get an overview of all flags you've raised, network-wide. StackApps post: https://stackapps.com/q/7173/43962
Review Stalker for Mith (works best in conjunction with "Review Stalker", later on) (broken after the changes to the review page)
Automatically opens reviews in a new tab when you load the /review page.
SFF Dark Theme
Makes Science Fiction & Fantasy a little darker (black background and topbar).
Allows you to leave stock comments to avoid typing out the same ones over and over again. StackApps post: https://stackapps.com/q/2116/43962
Link to chat profile from main-site profile
Adds a useful link to the chat profile for a user directly from their main site profile - uses chat..SE.com, so comes up with security issues, but is fairly easly to just allow it anyway.
Meta.SE rep helper (slightly buggy, warning)
Gives a summary of the user's network-wide rep + mod status on their usercard on MSE. MSE post: https://meta.stackexchange.com/a/153392/294691
Adds a scroll bar so that stars can be seen. MSE post: https://meta.stackexchange.com/a/213385/294691
Top bar in chat
Pulls the chat.SE topbar and allows you to see it while in a room. Useful for letting you know if you have new notifications or rep changes (why isn't this native functionality already?). Note: After a small topbar tweak, this broke, so install Shog's modified, fixed version instead: https://github.com/JC3/SEUserScripts/raw/3b07174bdb96a666db08d8153aee4c2388dec11e/ChatTopBar.user.js. StackApps post: https://stackapps.com/q/7404/43962
Turns raw SE links into title and link (but without your user ID for the share link, you'll have to manually add that) in comments
Automatically converts the bare URL in comments into the much more useful [link text](url) format. StackkApps post: https://stackapps.com/q/2378/43962
Stack Overflow Unoffocial Patch
Lots of minor bugfixes and the like. StackApps post: https://stackapps.com/q/4486/43962
Stack Overflow Extras (slightly borked after top bar changed, not sure if you'll be able to access the settings. Sometimes interacts strangely with top bar in chat)
Adds lots of helpful little tweaks (such as replying to yourself in chat, and a marker when a question is on the HNQ). StackApps post: https://stackapps.com/q/6091/43962
Review Stalker (broken after the changes to the review page)
Automatically refreshes the /review page every minute or so and tells you when there are new reviews available.
Programming Puzzles & Code Colf graduation theme script (since they still have the beta theme)
PPCG designed their own theme and created a userscript to use it. PPCG meta post: https://codegolf.meta.stackexchange.com/a/7955/65513
Global Review Summary
Gives you an overview of all reviews you've done over the network. StackApps post: https://stackapps.com/q/7723/43962
Chat history pagination
Currently there's hidden pagination in the chat history that you can get to by appending &page= in the URL. This script adds a GUI for that.
Room Owner message moving helper
Makes cleaning up after your bots in chat a whole lot easier. StackApps post: https://stackapps.com/q/7439/43962
Left-sidebar in the Topbar
I, uh.... have to admit that I don't exactly remember what this script does. It was written at the very start of Channels and the sidebar wasn't collapsible. I think it basically just collapses the sidebar?
Add timeline and revision links
Adds links to the timeline and revision history underneath a post, next to the "share" etc buttons.
Automatically encode and decode rot13 in comments
On Puzzling.SE, rot13 is often used in comments to avoid spoilers - this helps to automatically encode and decode. Puzzling Meta link: https://puzzling.meta.stackexchange.com/a/4651/25966
Unstar / unpin from the transcript
This script makes it possible to unstar and unpin chat messages from the transcript. You can't currently unstar something if it had already fallen off the starwall, so this allows you to do that.
Linkify deleted users
Links the "user" thing for deleted users to their deleted user stub, instead of having to manually type in the URL.
SEMTI (Stack Exchange Mod Tools Improved)
Moves a lot of the mod options for a post out of the "mod" menu and into buttons/links on the bottom of the post.
Desktop notification for new flags
Allows you to notice immediately when there's a new flag on your site (you need to keept the /admin/dashboard page open). Not recommended for use on Stack Overflow.
Add a handy link to reduce the number of clicks needed to destroy a spammer
If a user has a single deleted post or has a spammy profile description, this'll add a "destroy spammer" button next to "mod" and "account info" to make nuking these easier and faster.
Add the number of chat suspensions and annotations for users currently in a room and display that
This'll give you a rough overview of the current level of troublemakers in a room. If it shows a high number, that's probably not a great sign.
Move Mod Info (works best with the next script in the list)
Moves a lot of stuff around. I know, real descriptive.
Also moves a bunch of stuff around, especially the waffle bar.
Charcoal and SOBotics specific scripts
(not elaborating too much on these)
Flag Dialog Smokey Controls (Charcoal)
Autoflagging Information & More (Charcoal)
Flag Tracker (SOBotics)
Feedback Instantly, Rapidly, Effortlessly (Charcoal)
Natty Reporter (SOBotics)
Advanced Flagging (incorporates Charcoal and SOBotics stuff)
Target your !!/blame (Charcoal)
Smokey status (Charcoal)
SIM (Smokey Info for Mods) (Charcoal)