I posted a link to one of our newer games on Reddit (MegaTankMan, a Mega Man type game), and several of the users there pointed out that they game was hard to play with a keyboard. This is true for a lot of flash games, but unfortunately flash developers are limited to the keyboard. You, however, are not limited. There’s a program called JoyToKey that turns joystick/gamepad/controller input into keyboard input. All you have to do is set what keys you’d like each button to hit, and you’re good to go.
You can find the JoyToKey here.
Every joystick/gamepad is different, but I’ll run through the setup using the wonderful Xbox 360 controller. First, download and run the program after extracting the zip file – no installation needed, so if you want to keep track of it, place the folder on your desktop or somesuch. Make sure you connect your controller to your computer first or the program will yell at you. At least, I always imagine errors are the programs yelling at you. By default, JoyToKey won’t list every button that’s on the 360 controller, so we need to change a few settings first. Click the “others” tab on the right, and change the settings like so:

Now all you need to do is actually set the keys. Go back to the “Joysticks” tab. Each field listed there is a different controller button, and it would take some guessing to figure out which one each is, so here’s a list of most of them that you’d want to use:
Left Thumbstick Up = AxisY(<0)
Left Thumbstick Down = AxisY(>0)
Left Thumbstick Left = AxisX(<0)
Left Thumbstick Right = AxisX(>0)
Directional Pad Up = POV1:UP
Directional Pad Down = POV1:DOWN
Directional Pad Left = POV1:LEFT
Directional Pad Right = POV1:RIGHT
A = Button 1
B = Button 2
X = Button 3
Y = Button 4
Left Bumper = Button 5
Right Bumper = Button 6
To set them, just double click on them, hit the key you want them to correspond to, and hit OK. If you’re using a different controller, you’re on your own, but it shouldn’t be too hard to figure out. While you may not want to do this for every flash game you play, if you find one that you really like it can make it a much more enjoyable experience, especially for platformers.