I used to use a Thrustmaster PFCS along with Elite rudder pedals and a WCS Mk II throttle. When the PFCS finally died, I replaced it with an X-Fighter. All were great equipment for their time, but very bulky. The WCS throttle was also a terrible pain in the ass to program with its proprietary interpreted scripting language. I sold them years ago and haven't regretted it since.
Nowadays, I use CH Products midi/gameport Flightstick Pro, Throttle (non-pro version), and Pedals (non-pro version). They are almost indestructible, have an 8-way hat switch, and if you run Win9x the SpeedKeys utility is very easy to use for programming. Trim control on the stick also enables on-the-fly recalibration. I highly recommend them. The Flightstick Pro is also great because it is an ambidexterous stick.
Favorite DOS and Win9x gameport stick: CH Products Flightstick Pro, Throttle, and Pedals. If you don't want the whole HOTAS setup, just get the Flightstick Pro by itself, as it has a rudimentary throttle axis built-in.
For newer/modern/non-gameport systems, I have a Thrustmaster Top Gun Fox 2 Pro USB stick which is just plain awesome and also works flawlessly in Win98SE. It is probably my favorite controller. The ThrustMapper software is super easy to program. I also have the newer version of that stick, the "T.Flight Stick X". While very similar to the Fox 2 Pro, it has a few more buttons but almost no programming functionality. In fact, the old ThrustMapper software doesn't work with the new stick at all and there is no official alternative! The only thing you can do to program the newer stick is to use something like JoyToKey or XPadder. They work, but the old ThrustMapper software was much easier.
The Thrustmaster T.1600M looks like it is a better alternative and I wish I had known about it before I bought the T.Flight Stick X. It's also an ambidexterous stick, which is important to me. However, it will only work with WinXP and newer systems. So, if you want a new stick for your Win9x system, you might be stuck with the T.Flight Stick X and JoyToKey and/or XPadder.
Favorite USB stick: ThrustMaster Top Gun Fox 2 Pro
For gamepads, I have a Gravis Destroyer midi/gameport pad which works great. I also have a Gravis Xterminator pad which I've never gotten to work correctly, even when it was new. The software for it is just plain flakey. I also really like PSOne dualshock controllers. I've got a couple of those that I connect with a Radio Shack USB adapter. I also have a "Super Joy Box 5 Pro" USB adapter for connecting the Playstation controllers.
Favorite DOS gameport gamepad: Gravis Destroyer.
Favorite Windows USB gamepad: Playstation One DualShock with an adapter.