Unknown Legendoff his Harvest Moon album. Some powerful poetry goin’ on there…
Yeah, I hear ya. But I consider *Decade *as more or less a “greatest hits” album, so I figured that ruled anything off it out.
Remind me to tell you all the (fake) story about the time NYaCH came out to stay at my mom’s ranch and rehearse for a tour while Neil’s place was getting fumigated and I got to party and play with the band. 
Trying to define “Deep Cut” is probably going to be impossible, but in my mind a featured or lead single (single for my purposes being songs sent to/played on the radio and/or MTV and not necessarily official commercial singles) or song that was promoted by a major record label on a major album that under-performed is not deep.
Age and other things are going to color perspective. For example, “Sample and Hold” was the first Neil Young I ever heard and I SAW him performing it on TV. So, the Neil Young that looks like the “Trans” era dude was my first impression. I didn’t see him as a hippie or godfather or grunge or weepy singer-song-writer, but an 80s technology-era who might as well have been in Devo or Kraftwerk or something. Then, since my dad had every Neil Young album, I heard Harvest and everything else on the record player.
Going by that list on RS, I would also probably take exception to “Change my Mind” since it made a yearly top countdown of the top songs on my local mainstream rock station and was pretty well hyped after the Cobain thing. The (GOLD certified) album was #9 on the big chart and the single charted at #18 on the rock charts.
I’d probably go with something deep off “On the Beach,” maybe.
I wouldn’t say it’s one of my top 10 but I do like some of the songs. I love his remake of Mr. Soul on it for example.
One that hasn’t been mentioned that is his remake of “Farmer John”.
Time Fades Away was released in 1973 and still hasn’t been reissued. The whole thing is fantastic but LA, The Bridge, Last Dance, and the title track are my favorites.
Other great deep tracks by Shakey:
I Believe in You
Revolution Blues
Bad Fog of Loneliness
Pocahontas (electric version from Year of the Horse)
Little Wing (w/Crazy Horse)
Evening Coconut
I could go on…
There’s a Japanese CD, if you care to spend.
Oh, and it’s in an LP box set. Also spendy.
I’m the Ocean
Crime in the City (Arc/Weld version)
Star of Bethlehem
See the Sky
Walk On