I don’t know that I can answer this one really. I’ve played fantasy systems, but I wouldn’t ever really say that fantasy was my go-to roleplaying genre. I’m more into modern or futuristic games in the main.
I’ve of course played D&D (3rd and 3.5) but didn’t really find it an enthralling setting (though I do get occasional urges to go monkey with the spell system again). I’ve played Heroquest, Earthdawn, HERO Fantasy, and Warhammer Fantasy Roleplay (1st and 2nd). I’ve massively enjoyed some of those games, but I don’t know that I’d call any of them my favourite fantasy RPG.
Other games I have sitting on my shelf, or games I’m anticipating include Fireborn (the RPG of being dragons reborn as humans) and Karthun: Lands of Conflict which is based on the fantasy RPG campaign in D20 Monkey. Thing about Karthun is that it’s not actually an RPG, but a setting. It’s a complete rewrite of setting based around some of the ideas in D&D  with completely different takes on how things work – and the Kickstarter (which I backed) is also providing a GM’s book with guides on using the setting in various systems including FATE, 13th Age, Pathfinder, D&D 5th, Dungeon World, and Savage Worlds – I’m looking forward to getting my hands on the PDF to give it a look through.
To take a different tack, my current favourite fantasy RPG is Skyrim (yes, it’s a video game). I’ve not counted LARPs in this, where the majority of the LARPs I’ve played have been fantasy games and I am finding it difficult to decide which of Skyrim and Empire I enjoy most – it’s a tough call. Currently I think Skyrim wins because I don’t feel particularly extroverted at the moment and what I do at Empire requires a certain level of extroversion (which is a strange word).
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|1.||↑||this interpretation based on reading the webcomic|