As far as pure prog goes, I think only Abbey Road, especially the second side, can be considered for that, though a lot of their earlier music, experimental as it was, widened the boundaries.  Within You, Without You (raga/rock fusion--and a long song with a fairly long sitar/orchestral instrumental in the middle of it), Being For the Benefit of Mr. Kite, with its time changes, The Sgt. Peppers "overture" and "reprise" at the end, and A Day in the Life, with its use of orchestra, unusual structure, time changes, sound effects and sometimes complete disregard for pop music conventions--all share a lot in common with prog music.

I forgot to mention Roll Over Beethoven, which makes reference to a classical musician.  (Kidding.)  That's Chuck Berry, anyway....

Rubber Soul is the other that comes to my mind.

 

That's a song, this is an album poll.

 

Strawberry Fields and It's All Too Much were both available and Penny Lane would have worked very nicely too.  These 3 tracks would have elevated it into the stratosphere but it is, instead, dragged down by the inanity of "When I' m 64" and "Lovely Rita" - the first 20 seconds of Rita are so good the rest of the track is one of musics biggest disapointments for me.  Also, She's Leaving would be a really nice track on the White Album but is totally incongruous on Pepper.

 

Against all this Abbey Road is almost perfect (except Maxwell's Silver Hammer). 

 

Come Together and I Want You are strongly in the Progressive mould as is almost all of side two.  The Beatles ended on their highest note which is appropriate. We can only dream of what the next album may have produced.

 

 

 

For 1966 "Love You To" and "Tomorrow Never Knows" were very progressive with it's experimental/avant tape and microtonal Indian melodies. Both very bizarre sounding pop songs if you want to call it pop. Both tracks recorded before Pink Floyd and the Doors.  I would not count out the strings only "Eleanor Rigby", the very classically influenced "For No One", and the tricky time signatures of "She Said She Said".

 

 Sgt Pepper was very progressive on how the album was structured. Sgt Pepper was a non narrative concept album unlike Freak Out and the Kinks Face to Face. Sgt Pepper whose structure was unlike previous concept albums. The overture, the reprise, the finale, and hidden track was unlike previous rock concept albums. The tracks being linked with artificial sounds like crowd noises was also a future progressive rock trait. I have to say "A Day in the Life" is very close to being progressive rock and "Within You and Without You" is very progressive and basically alien to what rock groups were doing at the time.

 

 Really the most progressive album of the Beatles was Abbey Road with "I Want You", the synth Beethoven influenced "Because" and the big medley.

Believe it or not "Pet Sounds" by the Beach Boys was  a significant influence on the Beatles during the recording of "Sgt.Pepper" both from a technical as well as musical point of view, but "Sgt.Pepper" would not have been the same without  the precedence of  "Rubber Soul" (to some degree) and "Revolver". 

 

From a personal viewpoint in June 1967 i had enough birthday money to buy an LP, and was deciding between "Revolver" and the newly-released "Sgt.Pepper" - my brother's girlfriend already had a copy of "Revolver" so i plumped for "Sgt.Pepper" and hardly had it off the turntable for the next few weeks!  Many years later i still give it a spin and am still intrigued with it more than many other albums, but i still voted "Revolver" the most progressive for the foundations it laid for the future of Beatle music and rock.