Chemistry applications are tough because most of chemistry revolves around the actions of particles that cannot be seen by the naked eye. However, forensic science is always interesting and makes for a good lesson on the scientific method while testing for chemical compounds.
My idea is to pair the students up and give them a note card detailing an individual suffering from a list of symptoms and a description of what that individual does or where they live. The students will then investigate what compounds the individual may have been exposed to in that person's daily life. I will provide the list of possible compounds and the students will use knowledge of those compounds to narrow the list down.
Once a few possible compounds have been chosen, the students will go into the lab and begin testing for them. I will provide "contaminated samples" that the victim was exposed to and the students will test to see what comes up. The students will find what compounds the victim was exposed to and cross check them against symptoms of illness they cause to find out what is plaguing the individual. I would take a maximum of 4 days to complete the project because I'd really like the students to discuss the methods of investigation they'll use to solve this mystery. This'll also be pretty cool because it would be like an episode of House. And who doesn't like House?
Also, I'd like to add that chemicals that are found in many labs can be harmful if proper precautions are not taken. So my idea of allowing students to work with things like toluene (allergen), sulfuric acid (corrosive), or ammonia (eye, skin, nasal irritant) is not too "out there." I just feel as though I should clarify.
May the grace of the Valar protect you.