I've heard a few people complain about how there are "so many" different versions of the DVD.  In actuality there are only two.  Here's what it boils down to:  There are only two editions of each film, the theatrical edition and the extended edition.  The theatrical edition is a two-disc (film on one disc; plus one disc of extras) set and is available in two screen formats, fullscreen and widescreen.  The extended edition is a four-disc set (film spans two discs; plus two discs of extras) and comes only in widescreen.  It is available alone or as part of a larger Collector's Gift Set that includes a bonus DVD and a statue (or two) plus other goodies.  (The Fellowship of the Ring includes a National Geographic documentary about the film and a pair of scale replicas of the Argonath which are also bookends; The Two Towers includes a statue of Gollum and DVD about how the statues are designed; The Return of the King inludes a model of Minas Tirith and a DVD about the soundtrack symphony).  Both editions of the film are of course also available on VHS.  Of course, boxed sets of all three films, both theatrical and extended editions are now available.

One important note about the two DVD editions:  The extras included with the theatrical edition are not duplicated in the extended edition, so the "extras" disc in the theatrical edition is unique to that edition.  These include trailers and music videos of the end credits songs (Enya's "May It Be"; Emeliana Torrini's "Gollum's Song"; and Annie Lennox's "Into the West".)
 
 

The Fellowship of the Ring	The Two Towers
Theatrical edition DVD:   Widescreen  |  Fullscreen Theatrical edition VHS:   Fullscreen	Theatrical edition DVD:   Widescreen  |  Fullscreen Theatrical edition VHS:   Fullscreen
Extended edition DVD Extended edition VHS	Extended edition DVD Extended edition VHS
Extended edition Collector's DVD Gift Set	Extended edition Collector's DVD Gift Set
The Return of The King	Motion Picture Trilogy (boxed sets of all three films)
Theatrical edition DVD:  Widescreen  |  Fullscreen Theatrical edition VHS:   Fullscreen	Theatrical editions:  Widescreen     _|_     Fullscreen   Extended Edition:
Extended edition DVD: Extend edition VHS (not pictured) Extended Edition Collector's DVD Gift Set

What about the soundtrack CDs?

Well each soundtrack CD also comes in two varieties, a jewel case version (with multiple covers for each), and a deluxe Limited Edition with a faux leather gatefold cover.  The limited edition of The Two Towers includes a bonus track, which is actually a piece from the score of The Fellowship of the Ring.  The limited edition of The Return of the King includes a bonus DVD.  In addition to these, there is a boxed set of all three soundtracks.
 

The Fellowship of the Ring: Jewel Case edition Limted edition The Two Towers: Jewel Case edition Limited edition The Return of the King: Jewel Case edition Limited edition

The Lord of the Rings Motion Picture Trilogy Soundtrack boxed set