90s
SNES: Pretty good. The controller's a great and iconic shape; overall very comfortable. The only issue I have is that the D-Pad is a bit stiff, which is especially awkward to use in fighters.
Genesis: insanely comfy, but the 3-Button is kinda bleh due to having a small amount of buttons. The 6-Button variety, however, is pretty glorious for fighting games (combined with dat D-Pad).
Saturn: Regular controller is more or less as good as the 6-Button Genny controller (at least the western Model 2 one). However, the 3D Controller is surprisingly comfortable, and is the one I prefer for Saturn fighters when useable. Only issue is the Analog Pad; it doesn't feel as definite as the Control Sticks on the N64 or PS1.
Nintendo 64: It's alright for me. The layout does take some getting used to for 3D games, but I never suffered the extreme discomfort that many others have (Mario Party 1 notwithstanding). The only thing that super-aggravated me about the controller was how notoriously goddamn fragile the Control Stick assembly was. None of my childhood controllers have decent sticks anymore.
Oh, and gonna jam some third party and hacked controllers up in this bitch: The Hori MiniPad, though frightfully expensive these days, is a damn solid piece of tech that's sturdier than the OEM N64 controllers, and is
perfect for 3D games (but not 2D games, but I never played many games that required the D-Pad anyway). Also, getting a
LodgeNet control stick onto an OEM controller (not mine pictured) is glorious, seeing as the hotel controllers have amazing, GCN-style control sticks, and best of all are a fraction of the cost of Hori MiniPads at the moment (~$25-30 and some soldering are all you need).
Playstation(DS1): not a huge fan of this controller, and apparently I'm weird for it. The handles, though curved, "jut" out a bit too much and dig into my hands, making it uncomfortable for extended play. Not a huge fan of putting the "main" Control Stick lower either, or the nubs on the sticks being convex without grooves.
Dreamcast: I actually kinda hate this controller. The control stick is massively uncomfortable and feels like it'd be easy for my finger to slip off; the amount of buttons is pathetic for 1998 (though there are some 3rd party controllers that slap on a pair of C/Z buttons... why didn't SEGA themselves ever make one?), and the handles dig into my hands, especially at the end of the handles since SEGA decided to make them come to a point instead of a curve. Being that it got inspiration from the Saturn 3D Pad, it should've been a little closer to that formfactor IMO (especially having 6 face buttons again from the get-go).
Today Days
Gamecube: gonna have to jump on that bandwagon going on here; the GCN controller is essentially God's gift to gaming in my opinion. (In fact, I like GCN controllers so much I decided a couple months ago to collect all the basic retail colors that came out: Indigo, Indigo/Clear, Black, Spice Orange, Platinum, White, and Emerald/The-Best-Controller-Color-Ever). But that D-Pad... fuck that noise, especially for the Gameboy Player and 2D games. Otherwise, is my main SSBB controller.
PS2: (see PS1 above)
Xbox 360: I think this is almost as good as the Gamecube controller, but I just think that the handles don't fit my hands as well as GCN controller handles. (oh and just like the GCN the D-Pad sucks)
PS3: See PS1 and PS2, but there's also the oft-cited awful L2/R2 buttons.
Wii Remote+Nunchuck: It really depends on the game, but a lot of games that do the whole motion-control thing do it well, particularly the Mario Galaxy games and LoZ: Skyward Sword.
Wii Classic Controller: very reminiscent of the SNES controller, but a bit more comfortable due to curving from the sides to the back. For some reason I don't mind the Control Sticks here both being low (unlike the PS1/2/3). I like the old Classic Controller design a bit more than the Pro one. Used to be my main SSBB controller.
WiiU Gamepad: I was shocked at how comfortable this turned out to be, as I think many others were. It
is a bit awkward, granted, due to its size and shape... but then again you're bound to run into some snags at one point or another when you're slapping a bigass screen on your controller. I thought the screen would just be another gimmick, but it's come surprisingly in handy for me since my parents take the main TV fairly often.