Personally, I'll take educated, comprehension, silent running and jury rigging damn near every game

I don't find any perks to be essential now the DLC increased the level cap, before that educated was essential. The other perks are just good depending on your character. Some perks are more useful than others, but I don't think there's an 'essential' perk.

In Shining Armor.

Actually I take Light Step and Light Touch almost every time.

They help to reduce those SURPRISE!you're dead events.

Black Widow

Essential perks depends on the build. An energy weapons build would probably require vigilant recycler.