The most recent Marvel Handbooks started in 2004 and were limited to "theme" handbooks. That is, a handbook based on SPIDER-MAN or X-MEN or WOLVERINE, or MARVEL KNIGHTS, HORROR, THE GOLDEN AGE, AVENGERS, ETC. This lasted through 2005 and in 2006 the Marvel Handbooks went back to the rational policy of listing characters alphabetically for 12 volumes. In this 2006 edition they only listed characters that the 2004-2005 theme books missed, characters who went through major developments since 2005, or "new" characters who never even saw a Handbook entry in the last "Official Handbook" series, which was in 1989. They also released some sporatic "theme" books such as "Marvel Legacy" volumes that tackle a particular decade, MONSTER HUNTERS, MARVEL WESTERNS, THE 198, CIVIL WAR, PLANET HULK, etc. In 2007, they'll be released quarterly "update" volumes with more A-Z entries.
I believe there is a plan in place to make these into some sort of trade eventually, especially as the older handbooks were compressed into ESSENTIALS volumes, but I have no clue when this will be.