I always liked reclaiming Emprise du Lion. Pushing the Red Templars back and taking the Lion's Keep felt like a mini-military campaign, then freeing the villagers from the quarry, rebuilding the bridge and clearing out the three dragons. My favorite map and series of quests by far.
Story wise, I liked Leliana's personal quest the most. Anything involving Leliana, really.
For DAO, I really liked the Something Wicked. The orphanage was haunting, it felt so dark and twisted, and I actually felt suspense and concern the first time through, with all the unknown spookiness going on. It felt like I was in a Stephen King novel.
For DAI, I really enjoyed Promise of Destruction, it made me feel so emotional for Cassandra. She lost her friends, her apprentice, and most of her order. Then she learns the horrible truth about them. Playing as her LI or BFF made it so much more powerful.
In origins in would say the moment you meet the king and drink the blood and become a grey warden for the first time. And the ending where you get so many important choices
In da2 i loved the whole legacy dlc realy.
In DA:I i love the quest where you go after the well of sorrow with the puzzles and stuff (although it feels strange that you can take the time to do puzzles while your opposite faction is running straight for the well)
Also i loved romancing cassandra.. i like her personality..
I agree on the puzzles. I liked doing them, the concept behind them as it related to the story (completing the "rituals"), and found their inclusion fun, but their placement in that particular mission felt a bit odd for the reason you state. We're in a rush, trying to beat the red templars and Corypheus to the Well, and we stop to do puzzles?!
All of the other puzzles in DA dungeons to date have been more of the "do at your leisure" type.
DRAGONS!
Just kidding. But really. All dragons.
I love Wicked Eyes and Wicked Hearts as well as In Your Heart Shall Burn.
Now, LEAST favorite quest? Draining the lake in Crestwood. Ugh.
I liked "Demands of the Qun", I liked being able to see more of the Qunari side of things and see Bull react to save his guys.
Least favorite quest for me is everything in the oasis and everything in the exalted plains..DRAGONS!
Just kidding. But really. All dragons.
I love Wicked Eyes and Wicked Hearts as well as In Your Heart Shall Burn.
Now, LEAST favorite quest? Draining the lake in Crestwood. Ugh.
Focusing on the main quests here:
In Hushed Whispers had a pretty big impact on me. It was powerful to witness that possible future and the whole quest had a really sorrowful, hopeless feeling to it. I also found Alexius quite an interesting and even tragic villain. Also, that ending where the music picks up, your companions decide to sacrifice themselves, Leliana goes berserk mode... I got freaking goosebumps. Really great introduction for Dorian too.
I also agree with WobbleLikeAJelly that In Your Heart Shall Burn was really captivating the first time I played it. The music, the visuals and the atmosphere all worked well together. First proper introduction to our villain too. This quest is the one which made me really pumped up about all the possible things to come. (Too bad they really didn't live up to my expectations.)
When it comes to least favorite... well...
Many people seem to like it but I found Wicked Eyes and Wicked Hearts.... tiring. The premise was great but I thought the execution was rather clumsy. The hassle with the halla statues, the timed exploration and some downright sillyness like the Inquisitor leisurely climbing a wall while in clear view of the other quests. Or characters who are supposed to be veterans at playing the game (Leliana, Vivienne) practically doing nothing while the Inquisitor solves everything, no matter how ill-fitted for it from a roleplaying POV. That brings me to my other issue with the quest: there's a clear-cut "right way" and "wrong way". Your ability to RP is hindered since a failure just makes you restart, rather than actually having interesting consequences.
I don't feel like this because the quest would be hard or something. In fact my very first Quisitor got the highest court approval. I just think they could have done more with the whole "court intrique" theme since I somehow failed to feel it and found its' mechanics pretty unimpressive and tiring instead.
Still, I don't hate the quest and there's some elements/scenes I really like about it but generally I was still rather unimpressed and in each playthrough with a new character, I'm not really looking forward for it.
Favorite main quests are In Hushed Whispers and In Your Heart Shall Burn. I also like What Pride Had Wrought, but I'd like it a lot more if Morrigan wasn't required baggage. 
Favorite side quests, well that's a bit tougher since there are so many. Probably Still Ruins (that place is freaky), Dirthamen's temple (for the creepy factor, even if I get turned around every time I go there), Din'an Hanin for the elfy stuff, and Chateau D'Onterre for more creepy stuff and the various companion reactions it inspires.
Favorite companion quest: All New, Faded For Her since it always makes me tear up, and Dorian's romance quest for the amulet, especially if you bring him with you.
I thought both In Hushed Whispers and Champions of the Just were great. Here Lies the Abyss was my favorite, though, the subplot and level-design were both great, and having both an old cameo (GW companion) and old protagonist (Hawke) alongside your characters was awesome -- even if they did not bat 1.000 on every given Hawke's character.
I didn't enjoy What Pride Had Wrought's mission, but I love the Morrigan/Flemeth cutscenes that follow. I can totally dig RP-only assignments; I would have liked more of them from this game.
Trespasser had a really fun gameplay/combat mission, and I'm usually not into that.
Series-wide? I think Demands of the Qun (DA2).
All the Personal Quests (because of their Cutscenes) and everything to do with discovering 'Elvhen Glorious Stuff', love them old Elvhen Magic.
DAO: Urn of Sacred Ashes
I love Haven. It's such a creepy yet beautiful and historical place. Loved returning there in DAI (too bad Cory destroyed it and the temple!) I liked killing all those crazy cultists in the village and saving brother Genitivi from them. Also liked the choice to either let him come with you or leave him behind. My canon Warden sided with the Dragon worshippers and defiled the ashes. I love that you have the choice to do something like that to increase your own power. Exploring the Temple was fascinating as was meeting the Guardian and other spirits. That place had unique atmosphere that I really enjoyed.
DA2: The Bone Pit Mine
The best side quest of DA2. I like that it has many phases and that it lasts through all three acts. More side quests like this in the future games, please. I like Hubert, he's one of the best minor NPC's in the game and that's partly because his voice is so great. Good actor. That interrogation scene is especially wonderful and so amusing. DA2 had many funny humorous scenes and characters. I like that Hawke can become owner of the mine and create these ties and roots to Kirkwall since the beginning of the game.
DAI: Jaws of Hakkon
That whole main quest line of Hakkon DLC is one of the most memorable things about Inquisition to me. The DLC is so good and I was not really expecting that it would be for some reason (even though I saw awesome 5 star reviews and everything). I guess at first the story seemed like another andrastian Chantry thing that didn't personally interest me so much - so when I discovered the truth about Ameridan it was truly a shock to me (good one though). There was so many emotions my dalish Inquisitor was going through when she finally found Ameridan and realized he was of her blood. And even before that... just learning about Ameridan's life and his companions and seeing his story mirror hers in some ways. Finding Telana's remains and the spirit who had guarded her bones all these years. Learning the Aegis of the Rift was awesome, it's the best ability. Collecting Ameridan's memories, learning about his friendship with Drakon and some of the reasons why the Dales eventually fell... I loved all that.
Then the final epic battle against Hakkon Wintersbreath. I don't remember who said it - one of my companions I think - but Hakkon and hakkonites were really the reason why Ameridan couldn't return to Dales and warn the People, rally them to join forces with the Orlais and help them fight the darkspawn... So in a way killing Hakkon felt like a little piece of justice even if it was hundreds of years too late. I really like that talk with Scout Harding after you've killed Hakkon. It was JoH that made me love her. She's great. Everything that happened was just emotional rollercoaster for my Lavellan and I love it. That little island we got to visit was beautiful as was the ice fortress where we found Ameridan and Hakkon (and many other locations). That hakkonite shaman chanting the ritual to free Hakkon was also cool.
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