Loved this game back in the day, but one thing that bothers me now is that I can't seem to get an Xbox 360 controller to work properly with it. So I decided to use Xpadder, but for some strange reason unknown to me, Emperor's Tomb doesn't seem to respond to the Xpadder controls I set. Now perhaps I'm just overlooking something, but I'm pretty sure I know how to use Xpadder. Anyone gotten it to work with this?

I have the same problem!
I tried using both an xbox one controller and a ps4 controller.
Both work fine in other games but in IJAT the game doesn´t respond to the controller at all.
Just bought the game on GOG.com but refuse to play it with a keyboard and mouse.

Now I bought the game to my old original XBOX instead.

Let me understand. You were able to use the D PAD for alternating weapons and canteen and such? Also up and down d pad climbs rope? Does Right Trigger allow you to summer-salt? Please let me know!

Indiana Jones and The Emperor's Tomb (2003) XInput/Full controller support Fix
This fix is for XInput-compatible controllers only.

Buttons Layout Preview

All buttons work (D-Pad now works in the game menu and in the game itself).
Tips now display the Xbox buttons.
Button layout fully corresponds to the XBOX version.

1. Unpack content of archive to Indiana Jones and the Emperor's Tomb root directory and overwrite.
2. Run the game.
3. Go to the controls settings and turn on the controller.
Warning: Do not change the controller buttons in the controls settings!

Left Thumbstick: Move Indy/Navigate Menus
Right Thumbstick: Camera View/Climb Rope
A: Primary Attack/Menu Select/Menu Start/"ENTER"
B: Jump/Menu Back
X: Secondary Attack
Y: Action/Use/Interact/Menu Delete/Pull Out Appropriate Tool (Context Sensitive)
LB: Draw/Holster Weapon/Last Item Used/Drop Item
RB: Reload Ammo/Walk
LT: Look Mode/Reset Camera/Roll/Wall Peek Left
RT: Guard Mode/Focus on Enemy/Wall Peek Right
BACK: Draw/Holster Weapon/Last Item Used/Drop Item
START: Pause/Menu Start/"ENTER"
D-PAD: Inventory/Navigate Menus, Inventory Select (D-Pad Up), Holster Weapon/Drop Item/Inventory Close (D-Pad Down)

+ Widescreen Fix (Comparison Screenshot Preview)
Copy all content from this archive - IndianaJones_EmperorsTomb.7z in the game folder <path-to-game>\GameData\bin\
depending on the desired resolution.

+ Movies/Loading screens small size in full screen Fix
1280x960 (does not work with Widescreen Fix)
For Widescreen Fix-ed resolutions (The size of the video must be equal to the size of the resolution in which the game is started
You can convert the video to the desired resolution using The RAD Video Tools)

+ 30FPS Fix:
1 Go to <path-to-game>\GameData\indy\
2. Open default.cfg with a text editor
3. Set (or add) vsyncinterval:2

4. Go to <path-to-game>\GameData\indy\
5. Open vars.cfg with a text editor
6. Change fpsLimit=30 to fpsLimit=60
Notes: FPS over 60 may cause bugs in game.

+ Gameplay 4K60 Widescreen
+ Indiana Jones and the Emperor's Tomb Xbox vs PS2
+ Indiana Jones and the Emperor's Tomb PC vs XBOX vs PS2