If you plan on using mods in Skyrim, you will want to install and run
LOOT and
Wrye Bash so you can 1) put your mods in the proper order and 2) make sure that all of the mods that you are loading that modify monster/treasure/level lists all play together nicely and don't conflict with each other. If you're just getting into modding, that may seem a bit daunting, but LOOT is pretty easy to use, and you can find a good tutorial on how to use Wrye Bash
here.
You are also going to want to download and install
SKSE if you want to use some of the best Skyrim mods out there (such as SkyUI).
As far as Skyrim mods go, here are some of my favorites:
Run For Your Lives and
When Vampires Attack make citizens run AWAY from dragons and vampires instead of TOWARDS them like they do in the vanilla game. This is a must-install as far as I'm concerned - unless you like seeing the streets littered with the bodies of NPCs, of course.
Better Magic - This mod that modifies magical spells and perks in Skyrim so it is better balanced against melee and bow users. It doesn't add any crazy spells or anything; it just aims to make spellcasters suck less and makes it easier to manage upkeep on Alteration spells. You also don't have to rely on Impact to stunlock enemies as a Destruction mage.
Conjure Rideable Ethereal Horse - You'll never have to worry about your horse dying after you install this mod. This spell allows you to summon a spectral horse almost anywhere - even in towns and dungeons - and it's much faster then the standard horse. You'll also want to download the patch
here that keeps it from drawing aggro from guards when it is summoned or you dismount from it.
Immersive Armors - A compilation of custom armors compiled by hothtrooper, this mod is invaluable for Light Armor users that don't want to be running around in Elven or Glass Armors from the mid-point to the end of the game. That's not to say that it doesn't have great Heavy Armors either, but almost all of the Heavy Armors look cool, while the Light Armors leave something to be desired. I *would* also recommend
Immersive Weapons, but it frankly doesn't meet the same level of quality as Immersive Armors right now, though hothtrooper has started that he (?) plans on cleaning it up at some point in the future.
Skyrim Immersive Creatures isn't *quite* as immersive as it purports to be - you'll need to go into the options menu to switch it to "Purist" and then turn off Ore Elemental spawning - but once you do that it adds some additional enemies and random spawns to the game that make things a bit more interesting. It also adds some new summon spell tomes to the game that can be found scattered throughout the world.
Complete Crafting Overhaul Remade - The central piece of a series of crafting overhaul mods that include Weapons & Armor Fixes Remade, Clothing & Clutter Fixes, and Smithing Perks Overhaul Remade. It also incorporates Bandoliers - Bags and Pouches, JewelCraft, and JaySus Swords in its code; you'll just need to load the textures for those mods, and then you can unload the ESP files that came with them and let CCO Remade do the heavy lifting. Also has special patched versions of Cloaks of Skyrim, Heavy Armor, and Winter Is Coming. Does an excellent job of re-balancing the crafting system and fixing some of the bugs that the designers did not address whenever they shipped the game.
Cutting Room Floor - Like the title implies, this mod restores some NPCs and quests that weren't finished in time for the game to ship. Some quests were too complex or didn't have enough voice acting recorded to be restored, but there's enough extra content to justify installing it.
Civil War Overhaul - Turns the relatively static and staid Skyrim Civil War series of quests into an actual military campaign where you not only have to conquer enemy holds, but you have to make sure that you can defend your own. You can actually lose Civil War battles now! *gasp*
Atlas Map Markers = Pretty much the best map mod out there. Reduces the size of icons on the map to make it easier to fast-travel to specific shops and areas inside of cities.
Dragon Combat Overhaul - Makes dragons a more difficult to fight, but also allows you to shoot them out of the sky, typically with hilarious results. Alas, they still tend to wander off and attack other targets like they have ADD as soon as another target (any target) within range appears. Supposedly makes Alduin super-powerful, but I haven't tested that supposition just yet. On a side not, I don't recommend installing
Deadly Dragons; DD just makes dragon fights tedious and they tend to use abilities that kill everyone in the area before they can get to safety.