IMO the 1980 Special Edition is not good. This (I think) was the version that the studio released to fill the gap left by 1941 being a big flop in 1979. All the humour was taken out and the awful scene inside the mother ship was added at the end - which completely spoiled the awe and mystery.
The Collectors Edition is more like the original theatrical version.
In the Collector's Edition, Spielberg removed the mothership interior scenes and the film is much better for it.
Trust me; don't get the special edition.
The Bluray also offers on screen popups informing you which bits are different to the version you are currently watching and points out which shots are unique to the one you are viewing.
The Bluray also has all 3 on one disc.
The cinema version is the best version.
The extra money for the SE was given to Spielberg on condition he showed the Mothership interior - IIRC part of the deal was also another film being funded.
The SE was the only version in circulation for years.
The cinema version was only shown on tv once before the SE replaced it and the SE was the only one to come out on video.
The Collectors edition is Spielbergs preference but its not really any better than the cinema version.
Apart from effects films should never be altered later on unless its adding footage removed during the making of the film.
At least he didnt bodge it up like he did with E.T.'s 20th Anniversary cockup