My favorite arc is the Yorknew City arc.
If I would rank all the Hunter x Hunter arcs from my most favorite to least favorite, my list would go like this:
NOTE: Number 1 being the highest ranked arc or my most favorite arc. I also won't be including the arcs that are not yet finished because depending on how the arc ends I might rank them higher or lower. I'll be basing my rank on the completed arcs for now.
01) Yorknew City arc
This arc was godly, almost perfect in my opinion.
I loved all the fights in this arc, plus this is the arc where the Phantom Troupe was introduced.
The requiem for Uvogin was so sick.
The fight between Chrollo and Zeno & Silva was one of the highlights of this arc. Their fight was so short that it made me crave for more. I'd love to see Zeno and Chrollo fight one on one. It was such a treat witnessing Chrollo & the Zoldycks in action.
The fight between Kurapika and Uvogin showed us how terrifying a Nen ability with vows and limitations can be. Kurapika's Chain Jail rendered Uvogin helpless, it was a one sided fight. That fight let the readers and viewers know that in Hunter x Hunter, even the good guys can become merciless at times.
My favorite fight in the Yorknew City arc was the fight between Uvogin and some of the Shadow Beasts. "Everything from my neck up is all I need to defeat you." Nuff said.
02) Greed Island arc
Togashi totally impressed me with this arc, at first, I thought that this arc was going to be boring but Togashi proved me wrong. He did one hell of a job creating this arc, it was pretty interesting. I didn't expect that an arc based on a card game would work so well. After witnessing this arc, I didn't doubt Togashi's work anymore, I am now aware that every arc he makes will deliver and will surely don't disappoint us.
The highlight of this arc would be the dodgeball game against Razor. It is one of the reasons why I like Hunter x Hunter, a dodgeball game with Nen is so freakin' cool. I'd love to see a dodgeball game between the Phantom Troupe and the Zodiacs. xD
03) Hunter Exam arc
Damn, when I think about this arc, it kinda makes me want to see the four main characters together again in the future arc/s.
I loved every phase of the exam. I believe that the Fourth Phase of the exam was pretty awesome. But if I have to pick which phase of the exam is my favorite, I'd choose the Final Phase. Hanzo and Gon's fight impressed me a lot. We all thought that their fight was going to be a one sided match in favor of Hanzo, but man we were wrong. Gon managed to turn the tables around not just by overpowering Hanzo. He used an odd way of winning over Hanzo. I really liked how Hanzo explained to Killua that he didn't let Gon win but Gon won him over. Their fight was sick. For me, their fight is one of the best fights in all the anime fights that I've watched.
04) Chimera Ant arc
Most people might wonder why I placed this arc fourth in my list. It's not that I think this arc is lower than my top 3 Hunter x Hunter arcs (in terms of quality and writing). It's just that, there are things in my top 3 arc that I liked more.
Honestly, there were lots of things that happened in this arc that I didn't expected (like Meruem dying through poison, witnessing a creative Nen ability like Knuckle's A.P.R., Kite's death, Pitou ruthlessly killed by Gon-san, seeing some Phantom Troupes in action, etc.) and I liked it a lot since the this was pretty unpredictable.
Another thing that I enjoyed in this arc was Knov's palace infiltration. When Knov was infiltrating the palace, I was at the edge of my seat. I was saying "Get the crap out of there!" repeatedly. It was really intense. In my opinion, that was one of the highlights of this arc.
Another great thing about this arc was witnessing Netero's 100-Type Guanyin Bodhisattva. It was so freakin' cool, it was jaw-dropping.
I could list more great things about this arc but I guess I'll stop since I don't want to make my post any longer. xD
05) Heavens Arena arc
This arc changed my opinion about Hunter x Hunter from cool to pretty awesome. The moment Nen was introduced, I was really impressed by the Nen system. It was done quite well and made the future fights much more interesting and awesome.
The highlight of this arc is definitely the battle between Hisoka and Gon. It was pretty intense. I believe it is one of the best fights in Hunter x Hunter.
06) 13th Hunter Chairman Election arc
The main reason why I loved this arc is because The Oreo had his moments in this arc. It is such a treat when The Oreo gets more screen time. When The Oreo is around, he always deliver and does not disappoint you. Can't wait for the manga to continue. It's The Oreo's time to shine. For those who didn't like The Oreo before, after the current arc is done, don't you dare call The Oreo your favorite among the four main characters.
Oh, wait! I almost forgot. I loved that scene where Illumi goes into bloodlust mode. Back in the Hunter Exam arc, most readers/viewers thought that Illumi was afraid of Hisoka. That bloodlust scene in my opinion proved that he is not afraid of Hisoka. I am not saying that Illumi is superior to Hisoka or anything. I'm just saying that Illumi is definitely not afraid of Hisoka.
07) Zoldyck Family arc