Can anyone recommend me some mods that work well in the game that it feels like it has always been there (if you know what I mean, not tacked on and feels out of place) I want them to work togeather, I can think of a couple off the top of my head:

Horse Armor
Wildlife/Dungeon Sounds

Anything else? I don't mean graphical, I mean gameplay wise but feels polished.

Thanks guys, if i can find anymore I will let you know : )

Basicly you mean immersive and lore friendly mods?

Try go to Skyrim Nexus. Go to the category section and search for immersion mods. I usually list the mod after endorsment.

You may need to expand upon what you are actually looking for.

Do you want large mods such as http://skyrim.nexusmods.com/mods/9494 or http://skyrim.nexusmods.com/mods/10175?

Basic needs mods like http://skyrim.nexusmods.com/mods/11163 or http://skyrim.nexusmods.com/mods/17416?

Possibly environment changes such as http://skyrim.nexusmods.com/mods/17605?

All of the above, I just want them to feel polished and high quality and also work togeather (I know it sounds like alot to ask but I would prefer mods that helps my game feel like a better game, rather then just a huge sandbox for me to try things in, AKA Garys mod)

-shill, shill, shill-

http://skyrim.nexusmods.com/mods/17353

May or may not be what you're looking for - spell and power mod that expands on some of the NPCs and places the spells around the world in mini-questlines.

Alrighty then,
Here are just a few mods in my load order that stand out as being fantastic additions to the game.
Some are more involved than others but all of them have changed the way the game plays in positive ways for me.

http://skyrim.nexusmods.com/mods/10037

http://skyrim.nexusmods.com/mods/4955

http://skyrim.nexusmods.com/mods/18436

http://skyrim.nexusmods.com/mods/15786

http://skyrim.nexusmods.com/mods/12110

http://skyrim.nexusmods.com/mods/17723

http://skyrim.nexusmods.com/mods/12798

http://skyrim.nexusmods.com/mods/6770

http://skyrim.nexusmods.com/mods/5624

http://skyrim.nexusmods.com/mods/436

Just to name a few.

There are plenty of fantastic mods to be found, just go onto the nexus and check out top 100 and i'm sure you will find plenty more.