Ditto on the UPs and SkyUI. And don't forget SKSE (Skyrim Script Extender - http://skse.silverlock.org) and BOSS (http://skyrim.nexusmods.com/mods/6/?). Whether you use NMM or some other mod manager is kind of a matter of personal taste, but find one you like and use it. Manual mod management is very painful in my experience.
I'm rather fond of Categorized Favorites with a customizable overlay. The CFM funcitonality (http://skyrim.nexusmods.com/mods/4862/?) has been somewhat superseded by the current version of SkyUI, so I'd recommend seeing if SkyUI meets your needs first. If it doesn't I'm currently using an overlay made for SkyRe (http://skyrim.nexusmods.com/mods/25251/?), but it plays quite well without it. You may need to do some serious tinkering with the config file to make it lay out the way you want if you don't like its defaults. It's not difficult, but it can be tedious. Upside is that once you've got it done, it's done and you won't have to mess with it again. Downside is that SkyUI will fuss at you about it (there's a "don't nag me" checkbox in the CFM for SkyUI under "advanced").
Highly recommend "A Quality World Map" (http://skyrim.nexusmods.com/mods/4929/?); "Alternate Start - Live Another Life" (http://skyrim.nexusmods.com/mods/9557/?) - one can only endure so many cart rides to the headsman's block; and "Move It Dammit" (http://skyrim.nexusmods.com/mods/4020/?).
Anything else is going to be pretty much dependent upon how you like to play the game and what kind(s) of eye-candy you prefer (texture replacers, lighting, gameplay fixes and the like). My best advice is to head for the Nexus and dig through the the "Most Endorsed Files of All-Time" (Files --> Top Files). Plug 'em in one at a time and check to see whether you like them with a new game each time you add one (another reason to recommend Alternate Start). Disabling mods in an existing game is a BAD THINGTM, so should be avoided whenever possible.
Aside from that, go for what you like and have fun with it.