These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Author's Saving Throw: A rather mild example. Though "Beth/Rest" has since become quite popular among the fandom, it was at first intensely divisive due to its Retraux style and use of Auto-Tune- nobody quite knew how to react to it. Vernon responded by performing an entirely acoustic version featuring just him and a piano. This version is universally beloved, even among those who didn't like the original.
Colbert Bump: They received one from Kanye West in 2010, when he sampled "Woods" for his song "Lost in the World" from My Beautiful Dark Twisted Fantasy. Justin Vernon also contributed new vocals to both that album and to Yeezus.
8.8: The notoriously negative Robert Christgau's review of For Emma and (unusually) Allmusic's review of Bon Iver.
Ensemble Darkhorse: Song version. "Perth," "Flume," "Beth/Rest," and "The Wolves (Act I and II)" aren't singles but are fan favorites and get played live at most concerts.
"Re: Stacks," the climax of "The Wolves (Acts I & II)," "Beth/Rest," "Perth," "Skinny Love," and "Hinnom, TX.," not to mention "Holocene" and "Towers," which can induce Tears of Joy.
"Calgary" is probably one of the most haunting songs of the bunch.
If you listen VERY closely at the end of "Re: Stacks" (after the sound of Vernon standing up and walking away), you can hear him pick up a phone, sit there for a few seconds with the dial tone, then hang up. As if the song wasn't already heartbreaking enough.
Wangst: AVERTED. One would think an album called "For Emma Forever Ago" would be filled with this, but somehow it isn't.