First apps/mods IMO should be:
Nexus mod manager (incredibly helpful for installing stuff from Nexus, which has a lot of the mods)
Skyrim script extender (SKSE)-not really a mod per se, but an application that extends the game's capability and is requisite for a lot of mods
Unofficial Skyrim patch
More Hotkeys please (couldn't play the game without this personally and requires SKSE)
That is what I'd consider absolutely essential to a beginning modder (from my perspective).
An additional one that I'd highly recommend (takes a _bit_ to adjust to, but once you make the adjustment it is fantastic:
SkyUI