Hi,
I hope it is ok to post here. I know the poll says it closed long ago, but I see people posted long after that. So I thought I would add my 2 cents, seeings how I just completed these games and I wasn't around when the poll was done originally. If I've made a mistake in posting here, please forgive me (I know some people have strong feelings about posting to older threads, but hopefully it is ok in this case).
Anyway, what I thought was the best, in order (favorite being PoR): PoR, TotSF, GttSF, DKK, CoK, DQoK, PoD, CotAB, SotSB, Heirs. I haven't yet played the BR games, but I plan on doing so in the very near future.
PoR: I think this was fresh and seemed to fit the original design of the engine the best of the series. I really liked the idea of reclaiming areas and the series of missions and such. The outdoor system was a good fit for my tastes, kind of vaguely reminding me of the Ultima games (Ultima IV was and still is my favorite game ever). Anyway, I originally bought the Apple IIe version, which was a horrible port - it forced you to change disks over and over when you were first loading it and I eventually gave up on it. I finally got the PC version a few years later (when I got a PC

) and really enjoyed it. I also got a copy for my Amiga and I've often thought that if I were ever to replay it, it would probably be that one because from what I've seen so far it looks like that version may be even better than the PC (although now I see there's also a FRUA mod that perhaps I should do instead).
TotSF: My 2nd favorite. I liked this version of the engine the best of all of them. The gameplay was great. I enjoyed the more non-linear approach and exploring, thought the outdoor system was fantastic, liked all the little extra things about weather and movement and whatnot, etc. Also, I though the area designs were particularly well done, very believable and immersive. There's the thing about the ship battle that was really cool. Etc. I thought entirely resolving then totally changing the plot towards the end was a little weird, but it didn't detract from my enjoyment of the game.
GttSF: Same basic reasons as TotSF. TotSF reminds me of an improved version of this one.
DKoK: The DL series was great and I thought this was the best of them. It had great gameplay and a really good story. As I've mentioned in my earlier posts, I found the DL character choices to be the most fun.
CoK: This felt very fresh and inspired, but seemed a little less complete at times than the later games (less stuff changed at the end of the game, fewer optional areas, etc.).
DQoK: This was a good one, but I didn't like some of the engine changes (in FRUA's case, it is ok because those are a small price to play for the the ability to play/design custom modules and there are some work-around's). I've always found Taladas very interesting, enjoyed the Time of the Dragon boxed set and associated modules. That said, I think I would have probably set the story in Ansalon to have it tie in more closely with the previous 2 games. The gameplay was great. I still don't quite know how to feel about that gnome cutscene near the end ...

As far as the engine changes, I had to wonder, after 2 previous games and the many associated hours of play in those games, why suddenly remove my custom icons and change the interface around on the last game of the trilogy? I was particularly irritated by the loss of my custom icons and it took me quite a while to stop using the "move" command and to use the "1/7" keypad instead of the arrows. I can't remember for sure, but I think this was one of the first to have the "load" command, which was a good interface change.
PoD: Very epic, had most of my chars up to 40th level. The FR series was the only set of games I've ever played with such a long lifespan on my characters, both in terms of the the 4 games and in terms of real years (did the first 2 in the 90's and the rest years later). I thought the game itself was very well done and liked that it had such a huge amount of content. That last battle was insanely difficult and I had to try it over and over and over before I finally won, but it was one of those things you remember so it was ok in the end. I didn't like in the plot that everything that had happened basically reversed itself at the end with almost no one remembering, but the game overall was fantastic. I still felt like PoR somehow had a better feel to it overall, though, so was the best of the 4.
CotAB: I enjoyed this, but for some reason it felt to me like the story somehow didn't fit into the engine quite as well as PoR. I didn't care much for the outdoor system in that one, felt like a regression from PoR. I was much happier when I got to the PoD/DL outdoor system and even happier with the GttSF/TotSF outdoor system.
SotSB: This one was a bit too linear for my tastes, but I enjoyed it quite a bit anyway as it was the first one I'd played in many years and I've enjoyed every game in the series, just some more than others. I thought it was an interesting story with some very interesting areas. The mapping was painful since the areas went on and on and got a little tedious because it tended to be some kind of repeating pattern system or something. For such a long game, I did not like the complete lack of an outdoor system, as it made it feel more enclosed and linear.
Heirs: I found it to be enjoyable but I read many posts here and have to agree that it was the weakest of the series. That said, I personally didn't think it was terrible or anything; I still enjoyed it. While I actually liked the lack of a clear path through the main plot (which helped make it non-linear and encourage exploring), I never found a plot link between the main plot and the very last dungeon; I had to resort to cheating by looking at the design. It seems that last dungeon suddenly appears towards the end of the game, but I couldn't find it because I had already explored there so had no reason to check it again and found nothing in NPC conversations etc. to lead me back there to recheck that particular spot. I was also disappointed that it started at high level given that it was intended as a new, default adventure so that didn't make much sense to me. I think the same plot would have worked fine at low levels. I was going to take the opportunity of a single game (no series) to play some non-humans and thus avoid the level limits, but I had to abandon that idea when I found it started at high level.
I played the games in the order: FR, then DL, then FRS, then Heirs. That order may have somewhat influenced my opinions here. For example, I had some trouble in PoR originally (getting used to the game), so my characters weren't as interesting as those I designed later. I may have had more fun with PoD if my characters had been less plain (3 fighters, 2 clerics, and a MU). By the end of PoD, they had already been losing XP to the level 40 max for quite a while.
Sorry for the long post. I have been so into these games for so many years that I enjoy the opportunity to share some of my experiences.