I'm trying to think of any non-trackball / non-wheel / non-paddle stick-based arcade games that used analog controls from a retro time-period, and the only one I'm coming up with is Afterburner.
MAME can answer that question, more or less.
Under the MAWS deluxe search, change 'controls' to 'stick' which is MAME-ese for analogue joystick/yoke. You get this list including things like 720, Enduro Racer, Paperboy, SW/TESB/ROTJ, Space Harrier and Thunder Blade to pick a few classics.
To respond to the original question about joysticks, a lot of people build their own arcade sticks. The parts are readily available and the build doesn't need to be hard.arcadecontrols.com is a great resource and community for scratching that itch.
The truth is though that every type of home system is/was different, and the controls that suit a Commodore 64 and nothing like what suits a SNES, or an N64. If you're trying to recreate original-feel controllers for even a handful of emulated systems, it's going to be a lot of hassle obtaining them all, let alone getting them to work. A decently-made fighter stick plus an X360 controller should be enough to cover most bases most of the time.