Something

It has to be the songs that they gave away like "I'll Be on My Way" and "From a Window". The former's original recording was finally released during the 90's:
Unfortunately, they never recorded their own version of the latter song. Here's the closest imitation of what it might've sounded like:

The most5b4 underrated imo are the songs they gave away. "Bad To Me", "World Without Love" and "Goodbye" were actually better than many of those songs they put on their own records.
Hello, Good Evening and Welcome!

I think Bad Boy from Past Masters Vol 1 is their most underated. This song rocks, and Johns singing is Great. Even big Beatles fans don't know about this song.

Free as a Bird. It's an awesome Beatles song but everyone kind of forgets it exists because it came later.
Witty closing remarks have been replaced by massive head trauma and severe hemorrhaging.

george's blue jay way

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Another underrated song is
I'll Be Back
:
ThePrisoner,Buffy,LOST&Alias!

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I didn't know it was hated either. I really love this song. I think it sounds like in a dream and expresses very well George's sleepiness. (But maybe that's only me, and I love all Magical Mystery Tour anyway !)

I never knew people hated "Blue Jay Way"it's definitely up there for me. It's at least one of my favorites on MMT, anyway.
I see you've decided to go psycho. Godspeed.

I completely agree with you on "What You're Doing". I also think "Long, Long, Long" and "Misery" don't get enough attention. Tracks from
Beatles for Sale
are usually underrated. ("I Don't Want To Spoil The Party", "Kansas City/Hey Hey Hey Hey!")
I never understood the hate for "Blue Jay Way", it sounds ominous and the way it slows down and picks up is pretty fascinating to me. Either that or I really love the entirety of
Magical Mystery Tour
.

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I'll say "I've Got a Feeling." Definitely my favorite on Let it Be, with some of Paul's best vocals ever. And it's also in my opinion one of the best uses of that experiment they used to do all the time when they would take multiple snippets of unfinished songs that they didn't know what to do with and make it into a single song.
"That is one nutty hospital"

I'll be the first to stick my neck out for "Maxwell's Silver Hammer."
Certainty of death, small chance of success. What are we waiting for?

TIME Magazine gave attention to Norwegian Wood in a 1966 article.

I agree with Norwegian Wood, it needs more attention.

What You're Doing
The Word
Think for Yourself
Should Have Known Better
I Want You (She's So Heavy)
Only A Northern Song
Baby's In Black
Yes It 5b4Is
Rain
And Your Bird Can Sing

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Most Underrated Beatles Songs:
Ask Me Why
Misery
There's A Place
Don't Bother Me
I'll Be Back Again
Any Time At All
Things We Said Today (live versions too)
What You're Doing
You're Gonna Lose That Girl
And Your Bird Can Sing
She's Leaving Home
Martha My Dear
Old Brown Shoe
I Me Mine

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I like MISERY a lot. It sounds great on the remasters.