The only one I can think of right now is “The Trees”, by Rush. It takes the forms of a classic epic of the progressive and/or psychedelic variety, where there are a couple verses and a long, drawn-our musical interlude, then a final verse or two. Only the song doesn’t even clock in at 5 minutes.
I’m sure others can think of other songs that seem like they are a lot longer than they really are (for instance the collected works of the Black Eyed Peas 
)
I have never decided whether Cream’s song “Badge” was too short or just right.
(This Song’s Just) Six Words Long by Weird Al Yankovic
I’m On Fire, Bruce Springsteen. Just as it gets going, it fades out.
Cristopher Guest noted that one of the hardest parts of writing Spinal Tap was creating songs that *felt * interminable.
Just a Song Before I Go
CSNY
Teach Your Children by CSN(&Y?). Only two verses.
Happiness Is a Warm Gun, by the Beatles.
I agree with Teach Your Children and Happiness is a Warm Gun: I also thought of Eleanor Rigby. The strings and background singing at the end make it seem like it goes on literally forever (i.e. the strings and singing symbolize all the other verses that could be written on that subject,) nearly turn it into an epic when it can’t be more than 2 1/2 minutes long.
How about Maybe (the theme song from “Life and Times of Grizzly Adams”) by Thom Pace? I always liked the song but it is just over 1 minute long.
Danny’s Song
I didn’t think there’d be a chance in hell anyone would beat me to this one! 
How in the hell is this song only a bit over two minutes long??? I used to think it was really really long, like Suite Judy Blue Eyes.
“Maybe” By Thom Pace is standard length on the 45- maybe over the show credits its only a minute?
And though the song is average length, I wish “Tin Man” had a second verse, and wish "Arms of Mary" had a longer intro.
Sweet Child O Mine by Guns N Roses had the chance to be one of the greatest rock songs ever. However, it goes through a couple of great verses and then fades into instrument solos and these lyrics repeated:
"Sweet child o’ mine
Sweet love of mine
Where do we go
Where do we go now
Where do we go
Sweet child o’ mine"
I want them to make it again with some additional content and drop the back filler.
Fleetwood Mac’s TUSK is a freaking great song, with all sorts of cool tribal muttering, a giant marching band, guitar licks, and of course the chant/shout “TUSK!” on every chorus… but it’s only about two minutes long, and it could probably have been at least as long as Paul Simon’s “The Obvious Child” and not worn out its welcome.
Not to nitpick, but the 45 is 3:36
Color My World by Chicago
It’s one of my favorite songs. I really should be longer.
This song pushes five minutes, but it feels closer to an eternity.
(It’s a mostly harmless YouTube video for those at work)
More or less all the songs on Bob Dylan’s ‘Nashville Skyline’ album. At least a couple of them fade out prematurely for goodness’ sake…
Pearl Jam - Wishlist. My favorite lyrics are in the last verse, which fades out a quarter of the way through. They usually play it live with the full ending, but always different lyrics.