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I know this quote was supposed to be uttered by Sigmund Freud (may not be definitely). What I'm concerned here is not 'who said it?' but the idea behind this quote/phrase and it's actual meaning.
I also googled extensively about it, finding only very confusing posts. For example, here and here.
I would be really glad to hear all kinds of interpretations that you've got for this quirky statement.
The point is that Sigmund Freud supposedly saw sexual references in everything. If you are not familiar with the ideas of Freud, or with the associations people have with Freud, the quote doesn't mean much.
Freud, the father of modern psycho-analysis, became widely know for describing mental problems that people experienced using classical references and sex to explain them. Most famous is probably the Oedipus-complex, the idea that every boy essentially wants to kill his father and marry his mother. Not literally, but Freud described that the father at some point necessarily becomes a boy's competitor, and the boy idolises his mother as a woman.
Basically, Freud explained just about all of human behaviour in terms of sex. So if I smoke a big cigar, I am trying to send a message about my penis. Similarly, some people figure that even a neck tie is a phallic symbol because of where it points.
Freud's work is one thing, what people made of it was another. The quote simply states that, although thanks to Freud everybody may be thinking that every more or less phallic-shaped object is a phallic symbol and has some deeper psychological meaning, sometimes a cigar is just a cigar, in other words, sometimes there is no deeper meaning or message to things. Sometimes I smoke a cigar because I want to smoke a cigar, and not because I want to convey a message about other things.
With an assumed starting point where it is agreed that a cigar can represent something other than just a cigar (and in the Freudian context, most likely a phallus and/or the act of smoking reflecting an oral complex) to say "sometimes a cigar is just a cigar" means that while a cigar could represent a phallus or the desire to put a cigar in ones mouth could represent an oral fixation, it might not. (Of course Freud had a bias here as a cigar-smoker and it's also possible that Freud's love of cigars did indeed come from some sort of oral complex. Or it could be seen as representing his thanatos-drive since it likely contributed to his jaw cancer).
By extension, the snow-clone "sometimes X is just X" says that while X could be a signifier of something else, it need not necessarily be read as such.
