The Roy Allen Smith sequels, (earlier ones) while was still very much light hearted in comparison to the original, still had an interesting "feel" to it that was a nice mixture of goofiness and some element of danger. Out of the Roy Smith ones, I have to side with the majority and say Land Before Time IV had the darkest theme. It dealt solely with Little Foot's grandfather dying, a bit more subtle racism (i.e. Ali) then Mr. Three Horn's, "Three Horns never waste water, but your herds do!" in the third sequel, and mostly darker scenes like what Cancerian Tiger said about Ducky, and the Land of Mists, while not as perilous as what the kids cross in the first film, still pretty spooky.
Out of the Charles Grosvenor movies, definitely Land Before Time VII, as it actually deals with kidnapping, lust for power, manipulating family members, sending part of a herd to their deaths, even if it was unintentional, it was still reckless and stupid, back stabbing cohorts, coming to terms that just because you may love a family member doesn't mean you have to agree with them and their actions.
In the end however, I'm going with 4.