Hmm...Of all the sequels, the one I saw the most as a kid was 4 (only had that one and the original film), and I thought it was awesome for giving Littlefoot a love interest. I know I saw 2 at some point, because I had vague memories of a sharptooth baby.
Then, when LBT 7 came out, they ran an advert for it in a kids magazine I was reading at the time, and I honestly went "Seven? There's seven of these films?". So over the next few days, I went to the video store and borrowed the ones I hadn't seen. 2 I liked, 3 annoyed me (bullies), 5 was great, 6 I got bored watching for some reason. I remember watching 7 and loving it.
The next year 8 came out. This was the last one I saw for a while, because I rented that and thought it was bad. When 9 came out I had stopped caring (I remember perhaps one advert, but aside from that nothing). By the time 10 came out, the adverts were everywhere and I noticed them, but I was also starting to pay attention again because I'd heard on the imdb forums that Littlefoot's father was in this one.
I didn't see it, but when 11 came out on DVD, my dad bought it because it included the first movie with it. I saw it, and thought it simple kids fare (although I despised that Girls and Dads song...that note at the end just sounds off to me). After a while, I wanted to see the films again and catch up, plus I hated the idea of only having "Part 11" on the DVD shelf, so I started tracking down the films from the stores. I got 5, 6 and 10 first, and despite my memories, this time I preferred 6 to 5. 10 was alright, but Littlefoot's voice actor annoyed me so much that I rarely watched this one afterwards.
I think I got the three-pack next, with the first two sequels (I liked 3 better this time). Dad tracked down 12 for me (and I thought it was actually pretty good) and I got 4, 7, 8 & 9 at a Christmas sale. 4 wasn't as good as I remembered, 7 was still great, I liked 8 better this time (although I didn't think Ducky's voice actor sounded right anymore), and 9 was ok. Finally, my Dad found 13 for me. I actually didn't find it that bad (probably because my method of watching these films is to muck around on my computer with the movie playing in the background).
Out of memory, I'd say 5 & 6 are my faves, followed by 7, 12, 2, 3, 8, 4, 9, 13, 11 & 10. I certainly agree with Dino-doug about the animation, I love the way the newer films look.
EDIT: Although, now that I think about it, one thing annoyed me about the DVD for 12; the unskippable adverts at the beginning. When I got it, I sat down to watch the film, and was greeted with 5 minutes of unskippable (although thankfully fast-forwardable) adverts for Barbie. At the time I went "Barbie?! LBT isn't a girls-only franchise!?"