Deadly Reflex: Allowed for shield bash, decapitation, and finishing moves.
Romancing of Eyja: Allowed the player to romance the maid and then she would become your companion. (shameless plug, not that I need it, but 500,000 downloads shows people really dig romance/companions)
Better Bows mod. Not sure if that is the one, but Beth admitted to being inspired by a mod that made archery do more damage and be more realistic.
There were a lot of companion mods. Too many to name. Now it appears you can recruit mercs, friends etc to adventure with you and they are much more diverse and capable than Oblivions stock companions.
Living Economy mods where traders only had so much gold. Saw that put into fallout 3and it's carrying into Skyrim.
Dual wielding mods.
OOO, Changed the leveling of monsters and NPCs to be more static but they still had some leveling. It also contained harvest flora, containers had an opening animation, and it made it so bandits never had glass or daedric armor, and gave wildlife an ecosystem, added packs of wolves and fish.
Hair/face/head/race mods. Loads of mods that made players and NPC's look way better, some with tatoos or face paint, etc. It's obvious people have a huge interest in this, so look at Skyrim. It seems they have greatly improved characters and options.
Loads of clothing and armor mods. It's said skyrim will have more armors and variety in clothing/armor.
AI. THere are a lot of mods that made an attempt to improve the AI. No psychic guards, mods that make NPC's flee in fear, mods that make enemies flank you or notice arrows are incoming, etc etc etc. It seems Skyrim has adopted a lot of this.
House mods. Fallout added a bunch of styles to the homes. Lets hope Skyrim has this as well.
Alchemy sorter mods. While we dont' know for sure in Skyrim if they have something like this in fallout new vegas there are cooking stations where you can make something from a recipe. So you don't have to place each ingredient manually, it basically is similar to the alchemy sorter.
There were various leveling mods which seem to have wormed their way into Skyrim, maybe not in whole, but parts of a few I can see for sure.
What's cool to me is that Bethesda will put something in, if it's appropriate and works well. So I plan on making more epic mods so I can hopefully have some influence on TES 6.
Can anyone think of any other mods which you've seen influence Skyrim?