Skyrim Script Extender [official site], or SKSE to its sexy friends, is one of the most useful tools for making Skyrim do all the things you want it to with all those mods you use. Yes, even those ones you keep in the folder marked My Faxes, on the other drive. It's now available on Steam as a free addon that will install to your Skyrim folder and, according to the description, automatically run whenever you load up the game.
You have to have the Steam overlay running to make use of the additional functionality, unless you can be bothered navigating to the folder and launching it separately. You can also still get the mod from its web download page, but what's cool about this is there's now no need to leave Steam's interface to get all your mods running. As the vast majority of complex mods use SKSE and many of them are present in the Workshop, this was proving a hassle.
One of the developers took to Reddit to explain why SKSE can't be on Workshop itself. Because of what SKSE does - adding code to Skyrim to let it handle more complicated commands - it has to be a separate app that installs to the Skyrim directory.
Obviously, any discussion of Skyrim mods on Steam now comes with a rather large amount of paid mod baggage. SKSE had to make a statement during the paid mods apocalypse about both never charging and never taking a cut of mods that used it. Some have taken its introduction to Steam to mean paid mods are coming back, but that was quickly dispelled.