Here's a few that I use.
Stealth Skills Rebalanced http://www.nexusmods.com/skyrim/mods/28418/?
Sneak Tools http://www.nexusmods.com/skyrim/mods/19447/?
You can also use an optional module in Combat Remastered to give you an inventing skill tree (can craft things like bombs, traps and the like)
I also use Skyrim Sewers which adds sewer systems to the big cities like Whiterun, Windhelm, Solitude and Markarth. The systems are pretty expansive and there are passageways that you can access to get to almost any area in the city without going through the front gates. Also useful if you want to make a quick escape from a city. There's also some nice exploration with unique loot as well.
http://www.nexusmods.com/skyrim/mods/14351/?