My season 2:
The 37's – Essential or optional – I think this is really the bonding of the crew as a whole.
Initiations – Optional? Essential at a push – sets up some Kazon stuff that's good to know.
Projections – Optional – Nice Doctor episode, but how much does it add to the over all thing... well maybe Zimmerman, so maybe Essential?
Elogium – Skippable or Optional – It's not a great episode, but the Kes revelations/Neelix behaviour maybe should be seen for context?
Non Sequitur – Optional – since it's one of the few good Kim episodes
Twisted – Skippable – Doesn't add anything at all for me.
Parturition – Essential/Optional – Important part of the Paris/Neelix friendship, but then without Elogium might not make sense to have it...
Persistence of Vision – Skippable/Optional – Nothing strikes as particularly needed about it, but one of our Janeway fangirls may be about to correct me on that one.
Tattoo – Skippable – I don't care what it reveals about Chakotay, it's rubbish.
Cold Fire – Essential? - Pretty important for Kes' powers
Maneuvers – Essential – For the (ret-conned) Chakotay DNA baby and damn important to the Kazon storyline.
Resistance – Skippable?
Prototype – Skippable? Maybe optional for Torres backstory?
Alliances – Essential – Kazon story line importance.
Threshold – Skippable - so bad even the show ignores it
Meld – Essential - for Suder
Dreadnought – Skippable, especially if Prototype is Optional since it's a variation of the same story.
Death Wish – Essential – Good episode and huge for Q Continuum.
Lifesigns – Essential – Doctor, Vidiians and also the start of the Paris undercover.
Investigations – Essential, maybe optional – More Tom being bad.
Deadlock – Optional with leaning towards Essential just cos I liked it.
Innocence – Skippable – because what does it really add?
The Thaw – Part of me wants to say Essential because of its outright TOS fun. But really Optional I think.
Tuvix – Essential or optional – It's notorious, an important story that always generates 'discussion' and Janeway's decision is epic.
Resolutions – I wanna say Essential because of my belief of Janeway and Chakotay get in on while marooned, but willing to accept Optional.
Basics – I'm putting the two parters together because you can't watch one without the other, even if the quality drops in the 2nd part like it does here. - Essential obviously.
I can't in any good conscience make Threshold essential. How about "Special mention: This is terrible, basically ignored by the show, but a big reference point for fandom"