Version 1.3 released, check the first page.
I forgot to mention in the readme the menu buttons for PC controllers:

POV angles and X/Y axes: up, down, left, right

1: toggle stuff (same as the A button on the DC)

2: cancel/back (same as the B button on the DC)

3: confirm for the menu, enter for the console (same as the Y button on the DC)

4: backspace (same as the X button on the DC)
You can also make any controller button behave like the ESC key by using the command "bind JOY1_12 togglemenu" (replace JOY1_12 with the desired button, of course). By the way, here's a list of the controller's buttons, axes, triggers and POV directions:
PCFirst PC controller:JOY1_LEFT
JOY1_RIGHT
JOY1_UP
JOY1_DOWN
JOY1_AXISZ-
JOY1_AXISZ+
JOY1_AXISR-
JOY1_AXISR+
JOY1_AXISU-
JOY1_AXISU+
JOY1_AXISV-
JOY1_AXISV+
JOY1_POV_UP
JOY1_POV_DOWN
JOY1_POV_LEFT
JOY1_POV_RIGHT
JOY1_1
JOY1_2
JOY1_3
JOY1_4
JOY1_5
JOY1_6
JOY1_7
JOY1_8
JOY1_9
JOY1_10
JOY1_11
JOY1_12
JOY1_13
JOY1_14
JOY1_15
JOY1_16
JOY1_17
JOY1_18
JOY1_19
JOY1_20
JOY1_21
JOY1_22
JOY1_23
JOY1_24
JOY1_25
JOY1_26
JOY1_27
JOY1_28
JOY1_29
JOY1_30
JOY1_31
JOY1_32
Second PC controllerJOY2_LEFT
JOY2_RIGHT
JOY2_UP
JOY2_DOWN
JOY2_AXISZ-
JOY2_AXISZ+
JOY2_AXISR-
JOY2_AXISR+
JOY2_AXISU-
JOY2_AXISU+
JOY2_AXISV-
JOY2_AXISV+
JOY2_POV_UP
JOY2_POV_DOWN
JOY2_POV_LEFT
JOY2_POV_RIGHT
JOY2_1
JOY2_2
JOY2_3
JOY2_4
JOY2_5
JOY2_6
JOY2_7
JOY2_8
JOY2_9
JOY2_10
JOY2_11
JOY2_12
JOY2_13
JOY2_14
JOY2_15
JOY2_16
JOY2_17
JOY2_18
JOY2_19
JOY2_20
JOY2_21
JOY2_22
JOY2_23
JOY2_24
JOY2_25
JOY2_26
JOY2_27
JOY2_28
JOY2_29
JOY2_30
JOY2_31
JOY2_32
DreamcastFirst DC controllerJOY1_LEFT
JOY1_RIGHT
JOY1_UP
JOY1_DOWN
JOY1_D2_LEFT
JOY1_D2_RIGHT
JOY1_D2_UP
JOY1_D2_DOWN
JOY1_AXIS_X-
JOY1_AXIS_X+
JOY1_AXIS_Y-
JOY1_AXIS_Y+
JOY1_AXIS_Y2-
JOY1_AXIS_Y2+
JOY1_AXIS_X2-
JOY1_AXIS_X2+
JOY1_A
JOY1_B
JOY1_C
JOY1_D
JOY1_X
JOY1_Y
JOY1_Z
JOY1_START
JOY1_TRIGL
JOY1_TRIGR
Second DC controllerJOY2_LEFT
JOY2_RIGHT
JOY2_UP
JOY2_DOWN
JOY2_D2_LEFT
JOY2_D2_RIGHT
JOY2_D2_UP
JOY2_D2_DOWN
JOY2_AXIS_X-
JOY2_AXIS_X+
JOY2_AXIS_Y-
JOY2_AXIS_Y+
JOY2_AXIS_Y2-
JOY2_AXIS_Y2+
JOY2_AXIS_X2-
JOY2_AXIS_X2+
JOY2_A
JOY2_B
JOY2_C
JOY2_D
JOY2_X
JOY2_Y
JOY2_Z
JOY2_START
JOY2_TRIGL
JOY2_TRIGR
QuakeDC-compatible button namesDC_DUP
DC_DDOWN
DC_DLEFT
DC_DRIGHT
DC_A
DC_B
DC_X
DC_Y
DC_TRIGL
DC_TRIGR
PC-compatible axis namesJOY1_AXIS_Z-
JOY1_AXIS_Z+
JOY1_AXIS_R-
JOY1_AXIS_R+
JOY2_AXIS_Z-
JOY2_AXIS_Z+
JOY2_AXIS_R-
JOY2_AXIS_R+
The "compatible" names makes sure the engine can recognize bindings from config files made for other engines. For example, JOY1_A and DC_A are the same button.
The PC version doesn't support vibration, sorry. I didn't implement everything I wanted, including a new controller configuration menu and independent console variables for each controller (both controllers shares the same variables).
Oh, by the way, the Dreamcast version is untested, so tell me if you find any problems.