I love this game although I admit it has its faults. I'm still on my first play-trough and have learned the mechanics of the game fairly well. Although there are lots of awesome mods out there that I cant wait to try, I want to keep a version of the game that reflects bethesda's vision and testing while at the same time improving that experience. I will list here mods that in my opinion make the game better without fundamentally changing the game. BY better I mean faster navigation of menus, less interruptions in combat, better inventory management, etc. Nothing that changes the balance of the game. If you know of more please post them here.
These are the ones I use:
1. http://www.skyrimnexus.com/content/modmanager/: Not exactly a mod but it really makes things easy.
2. http://www.skyrimnexus.com/downloads/file.php?id=667: We all now that bethesda simply ran out of time with the PC interface( or something like that). Inventory management in vanilla Skyrim is non existent. Because of this a mayor part of the game is broken. QD inventory is a quick temporary fix but it improves crafting and commerce by leaps and bounds. If you don't get anything else get this one
3. http://www.skyrimnexus.com/downloads/file.php?id=2730: JUst what it says. Instead of having "Iron ore", "SIlver Ore", "Gold Ore" etc it renames items like this: "Ore, Iron", "Ore, Silver", "Ore, Gold". It does this for many different items , but not for everything yet. Still fun stuff.
4. http://www.skyrimnexus.com/downloads/file.php?id=1598: I dont know how but this work without any noticeable performance loss. On of my favorites.
5. http://www.skyrimnexus.com/downloads/file.php?id=2356: this mod makes you go WOW sometimes. It improves the visuals of NPC's
6.http://www.skyrimnexus.com/downloads/file.php?id=3389#content: makes far away trees look prettier without performance loss
7. http://www.skyrimnexus.com/downloads/file.php?id=3288#content: makes patces of grass thicker. I have my grass view to 0 since I find this enhances performance, but I tried this and it does makes the terrain more lush.
8. http://www.skyrimnexus.com/downloads/file.php?id=436&navtag=file/images.php?id=436&tab=3: Only use this if you would like to read roadsigns. I know that as a default I can barely read them.
Well thats all I've got so far. Feel free to recommend any other mods that you think fit this categories. I'll try em for a bit for a quick compatibility check then I'll add them to the list. Once I'm done with this play through I'll go crazy with all the other wonderful mods out there that change the heck out of bethesda's vision. I cant wait

Edit: added mods suggested by the baer