Awesome. So it sounds like they need a whole gamut of challenges, encounters, and puzzles. Not sure how specific you're looking to get, and the details will probably change based on their levels/year.
At a quick glance though:
Potions -- spellcraft checks of different potions and poisons, alchemy checks to craft others, and maybe some knowledge checks on what potions are appropriate to what conditions. Role play elements would include clues and hints derived from past sessions/classes.
DADA -- gauntlet style challenge. Think Professor Lupin's final from year three. A few combats where survival and/or capture is as much or more the goal than kill. Toss in various monster knowledge checks for clues about weaknesses or vulnerabilities.
Care of MC -- more monster knowledge checks; some tweaked handle animal and nature/survival checks; maybe even some healing
Herbology -- as above for plant creatures; survival for proper harvesting; for all exams good role play and reference to past encounters, stories, and sessions should provide bonuses or automatic successes
Charms -- spellcraft and arcane checks to know the right type of spell for the right type of creature; role play gives bonus to Saving throw DC's
History -- knowledge history, local, nobility and other checks; maybe some simulated social skill challenges to deal with various types of encounters with "inerts"
Transfiguration -- knowledge checks again; using the right conjuration, transmutaion, or other appropriate school of spell to solve various puzzles/traps
