For me it's Gears, Mass Effect, and Final Fantasy. Oh, not counting portables.,,Golden Sun, Mario Kart, and Mario's various iterations.
Mine are Fire Emblem and Metroid Prime. I like the other Metroid games too, but the Prime series is my favorite. Assassin's Creed is probably my favorite non-Nintendo one.
Fire Emblem, but you don't get points for seeing that coming from miles away. I'm also fond of the early Final Fantasies and the Golden Sun series, and I'm one of those suckers who buys one Pokémon game of every new generation.
Ah Pokemon, I have an interesting relationship with Pokemon. It's definitely a favorite series of mine, but I have no clue how I'd place it. It's like, it exists independently of my favorite games list, but it's one of my favorite games anyways. It's... weird. I'm not really sure how to explain it. It's just a separate entity if you understand what I mean.
Pokémon exists on another plane of being. It is the game to end all games, and yet it slips my mind easily when thinking of franchises I play a lot.
Star Fox and Super Smash Brothers will always be awesome for me. Kid Icarus: Uprising was also amazing, so I've gotten into that series. I've always loved Pokemon, but I've never really loved the games. I grew up watching the early TV series, and I love it still, but the games weren't ever my thing.
I love Fire Emblem. One of my favourite series. I can also dig Sonic to a point, along with Mario, Final Fantasy.... I feel like I'm missing something but it will eventually come to me
Ah, yes, Castlevania. My other top series I enjoy playing. I prefer it over Zelda any day. Everyone should okay this at least once. Once I get a play station I will own the lords of shadow game(s). Soon
I'm playing through Xenoblade Chronicles now. I didn't want to put it because it's my first game in the series and I haven't even beaten it yet, but if the other ones are as good as Xenoblade they'll almost certainly get a place on my list.
Aside from Zelda my other favorite series would be Kingdom Hearts, with Final Fantasy as a honorable mention. Kingdom Hearts is just something magical, that always keep me going back to it, and truly speaking, depending on the hype I have for the series, Kingdom Hearts can overthrone Zelda, in my favorite list.
An old, guilty pleasure has to be the Seiken Densetsu series, aka the "X of Mana" series. The last...four?...games have been horrible and painful, but I still hold onto the hope for the series.
Besides the Zelda series, I LOVE Uncharted. It might even be higher than Zelda on my list of favorite game series. Also, The Last of Us is at the very top. I know it's not a series, but NaughtyDog is planning on making it a series, so why not? I also really like Assassin's Creed, Bioshock, and Fallout. And I guess Call of Duty, but unlike the majority of players, I like it for the campaign.
I loved Modern Warfare and Modern Warfare 2, but after that I feel like the series really fell off. My biggest problem is the matchmaking. It's so unbalanced and you either end up on a good team and kick ass, or you end up on a terrible team and do horribly. Xenoblade took me 90 hours or so to beat, and I didn't even come close to finishing all the quests. Thankfully, there's a new game plus and you can retain your level, abilities, and a good amount of your items. How far are you in Xenoblade Chronicles Double?
EDIT: Nevermind, I think I mixed up parts of the game. But yeah, there's a point where some quests become inaccessible.
Also Halo (still need to beat Halo 4 grrrrr), the Batman Arkham games, and really again anything the creator of Xenoblade/Xenosaga/Xenogears does. He is frieking awesome.