I'll go game by game and give reasons why I used each fighter in each game. You're going to see a lot of repeating characters on this list, as I try to stick to a core set of characters, and simply adding in new ones when I enjoy playing as them.
This list is in descending order of character usage in each game.
Smash 64:
: The Zelda series is my favourite game series of all time, and at the time of Smash 64's release, Ocarina of Time was my go to game, so because of that I always gravitated towards Link.
: Was more of a secondary then a main. I didn't play the original F-Zero , or F-Zero X at the time, so Smash was my introduction to Captain Falcon. I loved his over the top Power Ranger-esque appearance, and I really loved his moveset.
Melee:
: For most of my time playing Melee, I once again mained Link. But after playing against a bunch of tough players in my town over the years, I realized that Link just wasn't good enough to keep up with them, so I decided to switch to Marth. Now, I'm currently undefeated since I switched to him. Love his moveset to death.
: Like stated above, Link was my main for most of my Melee career, and I was pretty dang good with him. But currently he's been demoted to secondary.
: Funny enough, Roy was my secondary when I was maining Link. I just thought he was a cooler Marth with fire, and I was really bad at getting tippers back then, so I used him over Marth. If only I knew back then.
: My "have fun" character. Never used him seriously like I do in Smash 4, but man is Ganondorf a blast to play. Love his Melee design. Plus he's a Zelda character, so that alone did a lot for me.
Brawl:
: Strangely enough I first played Path of Radiance (my first Fire Emblem game) literally a couple days before Ike was revealed on the Smash Dojo website. I loved Ike in his own game, and since Roy was gone in Brawl, I decided to use him. I loved his moveset from the get go, and felt like it perfectly complemented Brawl's slower paced gameplay. Destroyed many friends with Ike.
: It's weird how I first started using Marth in Brawl, and went back and mained him in Melee. By now I had gotten a lot more accurate with my attacks, so I picked up Marth, as, once again, Roy was out.
: Still my "have fun" character. Not nearly as good as Melee Ganondorf was, but I still loved playing as the Dorf. Love his grumpy grandpa costume too.
Wii U/3DS: (based off of amount of KOs online.)
: After switching to him in Melee, I planned to main Marth in Smash 4 as well. But before he was buffed, I wasn't doing that well with him, so I dropped Marth and decided to once again main Ike. But once he was buffed, I tried him out again, and he quickly surpassed Ike as my most used Smash 4 fighter.
: My Smash 4 main before Marth's buff. I loved playing as Ike in Brawl, so I was ecstatic when I heard he was returning, and with his beefcake Radiant Dawn outfit to boot! Loved the subtle changes to his attacks. Defeating opponents with Ike is incredibly satisfying.
: I don't know why, but Smash 4's Ganondorf just clicked for me. He was no longer just my "have fun" character, but instead became a character I could actually do well with. Regardless, he's still a lot of fun to ply as.
: After barely using him in Brawl (although I used him in Project M), I finally got back into using Link in Smash 4 because of his numerous buffs. Plus his new fierce Deity costume didn't hurt either.
: Never played Punch Out!!, but I liked Little Mac from what I've seen in his Wii game. So I was pretty happy when he was announced. I'm either into strong punching characters, or swordsman when I play Smash, and Mac's move set definitely fits into the strong punching category. I lot of fun to play with.
: I was so happy to hear that our boy was returning to Smash. I enjoyed playing him in Melee, so I had to give Roy another chance. I like him much more this time around, as he's been semi de-cloned from Marth and sporting a pretty pimpin' new outfit. His new hitboxes took a long time to get the hang of, but once I did, he became a lot of fun to play. Maybe if he came out earlier he'd be higher up in this list.
: I've been wanting Cloud in Smash since 3rd party characters were revealed as a thing in Brawl. So you could imagine how hyped I was when he was announced. Although I try not to use him too much, as I feel kinda cheap when I do. (As you can tell, the only other top tier I use is Marth, but people get way more salty about Cloud.) I will use him every once in a while though. Hope to use him more in Ultimate though.
: Not really a character I avidly play with, but I choose Lucina whenever I'm having an off day and am failing to get tippers with Marth.