Well the obvious one that comes to mind is
Lucy In The
Sky With
Diamonds....at the time, they were accused of it being totally druggy and trippy and poor ole John had to come forward in the end and say "look, my son Julian made a painting". While people over-analysed that song, trying to wring every last obscure drug reference from it, it was innocently-penned, perhaps garnished with psychedellia for good measure - but it seems almost dangerous to stretch lyrics out of context to the point where all "truth" is lost.
The songwriting process is a mysterious one, I think even Paul has commented on how he has no idea how ideas come about...that it truly is a mystery. I kinda believe that once songwriters come clean and are encouraged to dissect each lyric in detail, it removes that 'air of mystery' and ultimately affects one's enjoyment of the song. Sometimes, it's really cool to know where a certain line comes from, but it's also nice to just have that mystique element there.
Heck, in the end, who cares what the lyrics are about, just kick back, relax, enjoy the songs!

I needed comfort of love just to get me some piece of mind.. wo-oh