Ah, one of my favorite subjects! First of all, I use joysticks exclusively for all my gaming. Once I got an NES Advantage in the late 80s, I never went back to game pads.
You seem to be talking about joysticks that specifically use or at least come close to actual arcade hardware. On a console, I really only demand arcade type hardware for fighting games. And when you go back to the 16 bit era and earlier, there's not much in the way of them outside of some SF2 ports.
But for other games, I actually prefer "home style" joysticks. Especially the carbon dot style sticks, because the controls are soft and comfortable. Like ASCII's classic NES Advantage, it's real smooth on the hands and it's still one of my favorite controllers. (I modded one to use on an Xbox for emulation) For the SNES, the SNES Advantage and Capcom Fighter Power stick are my favorites. I had a C&L Controls Championship joystick, and it was GREAT for those SNES fighting game ports like SF2 and Fatal Fury 2. The plastic housing wasn't too durable though, I managed to break mine. But for something like Super Mario World or Megaman X, I went back to the SNES Advantage. And by the way, I do have a Pro-Play Home Arcade for NES. It came with an old style Happ joystick, with little tabs between the actuator and the microswitches for a tighter throw; it was so nice I took those bases off and used them in a couple of arcade machines. But the whole time I used it (back in the day, *sigh*) it did feel rather strange to me, to play NES games with the heavier arcade hardware.
I'm still looking for a good Genesis joystick, though I'm procrastinating because I don't play the Genesis very much. (I keep meaning to change that- my new years resolution for 2010 will be to play more Genesis) The sticks I have are the Sega 6 button joystick, and the ASCII Fighting Stick SG-6. I don't like the Sega joystick. The ball on the stick is too large, and the throw is a little too wide for my taste. The worst thing is the buttons, they're not very responsive. There are a few times where I'll press a button and nothing happens, as I'm not pressing it hard enough. The start button is in an uncomfortable spot, and the whole thing just feels awkward. The ASCII stick is much better; just like the NES Advantage, it's got that same soft feeling carbon dot joystick with a nice tight throw, and the buttons are soft and responsive. My one complaint about it is that the base is too small, there's only room for my fingers, so both hands hang off the sides. A little awkward but I still find it more comfortable than the Sega arcade stick. It's great for shmups.
For the PC Engine, the only stick I have is the only one I'll need- the
ASCII Stick Engine. It's essentially an NES Advantage with select and run in the upper right corner, and a new paint job. (Black with green buttons) It feels just like an Advantage, so it's nice to have a controller I'm already familiar with. The XE stick for the Famicom is also on PC Engine, I'd like to give it a shot but they're pretty expensive. And I'd like to give that TG16 Turbo Stick a spin too.
My Saturn joystick of choice is the InterAct Eclipse stick. It feels a lot like an ASCII carbon dot joystick, a nice soft stick with a tight throw, and I use it exclusively for shmups. (Which is mostly what I use a Saturn for) For most other games, I use the Sega Saturn arcade joystick. It's got plenty of room for the hands and it's not a bad joystick, but the stick itself isn't as responsive as the Eclipse stick, but it's heavier, and feels more durable. Also the autofire is done with individual switches, so it's easier to set up than the Eclipse stick, which uses that "hold this button and press that button three times" nonsense.
For Dreamcast, I use the Eclipse stick with a Saturn/PS2>Dreamcast adapter. Because I only use my Dreamcast for shmups.
And for the PS1? I don't play much PS1 anymore, and when I do I'll probably use those ASCII arcade sticks that look like official PS1 hardware. They feel pretty cheap, and I certainly don't recommend them for serious fighters, but they're not
that bad if you're playing something like Asuka 120% or some platformer.
Oh, and I want to mention Neo Geo console joysticks, they're actually pretty damn nice. They're great for... well, Neo Geo games. I'd like to try one of those remade versions for PS2.
Again, all the above joysticks are for general gaming and I wouldn't use them for fighters. I stick to Happ/Sanwa arcade hardware type stuff for that; Fighting games demand durability in a joystick. And heck, I wouldn't actually use any of the consoles mentioned above for fighting games. Pretty much everything I want to play is available for Xbox or later systems.