In the game, it might work something like this:
The characters are faced with an underground chasm they need to get across. The chasm is clearly too wide to jump across by normal means. This is considered an "Average" challenge that is designed to net each character 300 XP when crossed.
The wizard casts fly and sails across easily. However, his XP is reduced by 300 XP for using the fly spell to circumnavigate the challenge. Basically, no challenge, no XP.
The monk takes several steps back and uses leap of the clouds to jump across. The monk gains a huge bonus to his jump skill, making it feasible to get across - as long as he rolls a 5+ on d20. However, the XP he gains is reduced by 150 for using the leap of the clouds ability.
The fighter moves forward, swinging a grappling hook with rope attached and secures the hook on the opposite side with a lucky throw. After shimmying across using a climb check with an equipment bonus, he gains the standard 300 XP.
Lastly, the rogue scales the side wall of the cavern and clambers up to the ceiling, where he makes his way across with his climb skill. Because he used the climb skill without the assistance of gear or magic, he gains a 100 XP bonus.