I'd dare to say that there are a few which are so essential they should be taken 'as read' - Unofficial Patch, SkyUI, iHUD, SKSE and SD, maybe a couple of others of a more 'advlt' nature

Apart from those, the three I miss the most when I'm testing stuff out on the semi-vanilla rig downstairs are:-
1) The Levelers Tower - becoming ESSENTIAL due to the number of new characters I've had to roll up recently, thanks for the patches Bethesda
2) Phanderix Magic Evolved - 'Phoenix Volley' and 'Glacial Volley' are the sub-machine guns of Skyrim! and
3) P.I.S.E. - Subtle, but it just adds so much to the feeling of a challenging experience.