Due to the high cost of securing music rights, the distributors of "The Wonder Years" and artists whose music appeared on the show have yet to come to an agreement. Original music rights agreements were negotiated before the widespread use of DVDs, thus the rights to use the music never extended beyond the original airings and syndication. Several television shows that have relied heavily on external music sources, most notably "WKRP in Cincinnati" and "The Wonder Years" therefore run into a problem, since the original agreements never included home video or DVD rights, thus the rights to each song must be renegotiated in order for the song to be included on the DVD. This can be very expensive, and can take many years. For example, the first season DVD of "WKRP in Cincinnati" released in 2007 omitted most of the original music in the soundtrack, since agreements could not be reached with many of the record companies. Therefore, music heard in the original airings and syndication was removed in favor of "generic" music, for which royalties are not due. For a show like "The Wonder Years," in which the original music is an essential part of the structure of each episode, music rights would have to be secured for each episode for each season, since using generic music would ruin the structure of the storytelling. The cost would likely run into the millions of dollars to secure tracks from "The Beatles" and other high-profile artists, which would cut into the profit margin of the DVD sales. This would reduce the profit margin significantly, thereby reducing the liklihood that a comprehensive DVD set would ever be released.
To date, there have been two 'best-of' DVD sets for "The Wonder Years" They are: "The Best of The Wonder Years: July 24, 1999" (1 Disc-2 episode set) and "The Christmas Wonder Years: July 24, 1999" (1 Disc-2 episode set). However, they are quite expensive and do not contain the original music.
Update: In february 2014, StarVista Entertainment/Time Life announced a complete series set with most of the original music would be released on DVD later in 2014.
Update: In August 2014, StarVista/Time Life announced they had managed to clear 285 songs along with the theme song, which was 96% of the music on the show. Because fans were concerned about that 4% of uncleared music, a complete list was released showing the 14 uncleared songs and their carefully picked replacements. [source]