I'm rather mixed about it, honestly. There were a lot of great scenes, though it felt like Dany and Theon got the short end of the stick. The climax to Theon's arch got turned into a silly gag(instead of the dramatic, holy shit moment it should have been), but the House of the Undying was extremely underwhelming. I really liked the Khal Drogo bit, but it's like they completely missed the entire point of the House of the Undying. The twist with Xaro and Doreah really seemed rather ridiculous--less a clever Martin twist, but a lame tv cliche drama one. No substance to it. . .but I think that's how most the Qarth adaptation feels. I think, taking into account all of the Qarth segement now the season is over, the producers over-reached a good deal more than they should in the "making-it-up land", and just really sullied what was a great, ominous shadow of future prophecies and uncertainly in the books(plus, no Strong Belwas

). They obviously must realize that Xaro shows up in A Dance of Dragons, so it just really seems like a dumb choice(of course, they could easily say he got out someone I suppose, but still, really lame). Not to mention poor Doreah. I don't think she really would have betrayed Dany. If they wanted to get rid of her, I don't see why they didn't just kill her off like Martin did. It would have made a good enough heartfelt scene. So overall, I think Dany really suffered the most as far as adapting the material this season. "Less is more" probably would have been better than trying make more stuff up to give her more scenes.
But, what's done is done, I suppose. I still believe they can get back to being more faithful starting with next season, so with perpesctive, I think the few misgivings of this season will be extremely easy to overlook in the future.
As far as my favorite scenes, I really liked the Tyrion scene with Vary's and Shae. So well done, as well as the Stannis-Red Priestess scene. Especially the ending shot.
The scene between Master Luwin and Theon was great as well.
I will kill that man. I don't care how many arrows they feather me with, or how my spears they run through me--I will kill that horn-blowing cunt!
And of course, the ending shot of Sam and The Other's was a great way to end the season. . .and remind the audience how the real threat is marching forward while the realm is fighting against each other.