A couple of mine are:
The Land Beyond Time (The Oracle, I think)-This fanfic is no longer available, but it had an intriguing, if not bizarre storyline. It combined futuristic and space elements with Land Before Time. It also included some interesting story plots that kept me wanting to read more, including Pterano being Petrie's father and Ali being tricked into thinking Littlefoot was evil. I would recommend to read it, but since the story doesn't exist online anymore, I can't.
Worlds Connected: Littlefoot's New Friends (JFalcon)-I'm not sure if this is still on FF.Net, but if it is, I recommend it, especially to sharpteeth fans. This was not only the first LBT fanfic I read that had chapters, but also the first one written that has sharpteeth good guys. So if you like to see sharpteeth heroes, check out this story.
A Sharptooth's Heart and A Sharptooth's Heart II (Keni)-This was the first story I read that involved an invented species of dinosaur. It's been a long time since I read the first story, so I'm sorry to say I don't have much to say on that. But the second one keeps me interested. This was the first fanfic I read that introducted the "sharptooth instinct" concept, and also the first one that introduces an ominvore character. It was this that helped inspire my Out of the Shadows fanfic. It's worth the read.
Battle of the Sacred Essences (Littlefoot1616)-The first well written fanfic I saw that involves humans as well as multiple crossovers. I stayed with this fanfic from beginning to end, being patient enough to wait as each chapter came out. Normally I would think crossing over too many elements would be confusing and a jumbled mess, but I feel Littlefoot1616 really manages to pull it off here. If you haven't read it yet, I strongly recommend you do.