Hmm, this is a tough one, for a number of reasons! First of all, the characters have changed so much from the sequels to the late sequels, especially Cera *grumble* (see my Cera rant from a few months ago for details).
In the original, it is extremely hard to choose a favorite character, as I found each dinosaur was very well-developed.
I have always had a liking to Cera's character in the early sequels, namely LBT 2 - 4. Cera posessed a unique, sensitive inside which was often masked by an entertaining outward character, often unwilling to show her true feelings to anyone but the audience.
I must admit, however, I haven't been very happy with how Cera's character has been protrayed from LBT 5 onward. She was fairly Cera-ish in LBT 6 and 9, but a number of flaws were apparent to me in her character throughout LBT 5, 8, 10, and especially 11. 11 was a very strange film for Cera.
I admit, I'm not always fond of the 'chemestry' between Littlefoot and the rest of the Gang at times. I often wonder about the intelligence differences, and why it's so often Littlefoot who is solving problems. I'd like to see the other characters play a more active role in the planning of problem solving in the series. I don't expect them all to be super-intelligent. Perhaps it seems that Littlefoot is Very intelligent, and may a little too intelligent at times.
I do like Spike's character, and believe the series would feel incomplete without him. His role is less obvious, but certainly important, and in some cases symbolic. The idea of a family bond between Ducky and Spike can be directly transferred over to how the members of the gang see each other, for instance.