This is a harder question that it should be> Then again I've played as and against countless characters for over 40 years and many of them have had incarnations outside of gaming that influence the decision beyond simply their in game appearances. Others have been amazing characters in games and series but have had some real stinkers either before or after their prime that prevent them from being a sure thing.
Pac-Man - Love the original and the early ports and the recent Smash Bros. version. One of my favorite records growing up was a picture album and Pac-Man fever was a real thing. My 6th birthday cake was Pac-Man thanks to a joint effort of both my parents. The first mini-arcade game, portable game and wristwatch games I ever saw were Pac-Man. But many incarnations, especially in 3D and "arrangement" versions sucked meaning most games released in the past 25 years were crap, so that knocks out the first thing that popped into my mind.
Link - The Legend of Zelda and Zelda II: The Adventure of Link were the reason I saved up and bought an NES. I loved everything Link and Excuuuuuuuuse me princess but I even liked the Legend of Zelda episodes of the Super Mario Brothers Supershow. Mario was a nobody compared to Link in my eyes. I didn't have a SNES or a Gameboy so missed out on what many consider some of the best releases and when I tried them years later I thought they were kind of meh. No CDi so I missed out on what many consider the worst releases. Orcana of Time was outstanding, still haven't tried Majora's Mask but then came GameCube. Wind Waker was so terrible I realized that despite the fact that I loved all things Link and Zelda I really didn't like the bulk of the series. Releases since have failed to impress and I just can't list Link as my favorite anymore despite the fact that for more than a decade I wouldn't have hesitated to.
Master Chief - I love the Xbox and nothing is more iconic than Spartan 117. I've read all the books, seen the movies, videos etc... The story and universe is amazing. But frankly he is simultaneously amazing and lacks any sign of personality or relatability. Too bland to be my #1.
So childhood consoles fail me, consoles of my teens fail me, and modern consoles also fail. PCs have had Commander Keen, Duke Nukem, Doom Guy, and countless others but they don't make the same connection. My WoW character is great but I wouldn't call that my favorite video game character as most of what makes my Orc Shaman unique is... well... me. So PCs fail me as well on this one. (Leisure Suit Larry had potential but Magna Cum Laude and several of the later ones fell flat for me.)
What does that leave? Handhelds? Sorry but Tetris blocks are not a good choice for this (or for a movie) and virtually everything in this space is a pocket version of the others.
This is tough. That just leaves... ARCADES!
I can narrow the choice to two. Dirk the Daring (Dragon's Lair) and Dexter (Space Ace). These two came along and introduced the world to games that were not pixelated screens full of bleeping and blooping and a handful of very limited sprites. No, these were Disney level animations that you controlled with full voice and sound. Sure control was limited and timing was erratic but this was mind blowing stuff that had crowds around every machine and lines out the door to play despite costing twice what any other machine in the place asked (it even made the soda machines blush). it has been ported to nearly every platform that can handle it, and titles inspired by it were made for those that couldn't. Sure some versions, especially the inspired titles, were poor imitations but even they had a charm to them and the full versions, or near full versions, were almost always among the most impressive things seen on their respective systems at the time. The cartoon was enjoyable, compared to others of the time, and the comics are great. I've made the effort to meet Don Bluth in person to get his autograph and thank him, I've yet to do that for any other game programmer, publisher, or artist so there's that as well. I've probably spent more on various versions of these games and memorabilia, vintage marketing materials, and anything else I can get related to them. So I think they are a safe choice.
And if I had to choose between the two I would have to go with Dexter. The sci-fi setting, roller disco, his ability to talk and not just gasp and grunt like Dirk put him over the top. Besides Kimmy > Daphne and while Singe > Borf it is offset by Borf > Mordroc.
So there you go. After much thought ad deliberation my favorite video game character is named Dexter.... wait this can't be right... I demand a recount.... *several hours later* well I'll be... all hail Dexter!