Pressing Esc will take you to the main menu where you can configure most controls. If your mouse has a scrollwheel, be sure to use it to zoom out a bit too — this resets after every load game though. Most players find it easier just to use the keyboard though.
If you are having trouble picking up an item press (the use key) left Ctrl + ↑ to pick it up. Transferring items from/to chests and NPC shopkeepers etc… is usually Ctrl +→ or Ctrl +←.
Have a fiddle with the settings in the game and get a feel for whatever works for you. Jump only works when either moving and pressing jump or if you are standing against a wall/cliff and press ↑ at the same time. If the slope is less than (say) 80°, you may not be able to grab it even if it looks like it'd be a cakewalk.
If you'd rather play using a gamepad, you can use a third-party utility such as Joy2Key (don't confuse the Linux and Windows versions, as they are different programs with the same name, though they share a similar purpose) to map the gamepad controls to keyboard key presses. This works pretty well, as there are only about a dozen important controls in the game in total.
In any case, be careful, as certain key combinations (such as Ctrl + Esc ) may cause the game to crash if accidentally pressed.
Chart
US 104 key
Spell
Sheet
Log
Key
(Marvin)
- Legend