CT is good for visceral structures. Small bowel, Large bowel, stomach, pancreas, liver, etc.
MR is generally better for soft tissue (neck, bone, ligaments, extremities)
CTs are quick and easy and are generally preferred in trauma or acute situations.
Overall, MR is a better quality picture and doesnt exposure the patient to the radiation. Remember your patients who CANNOT have MRIs (pacemakers, etc).
If you need quick answers, get the CT. If you need a bit more detail and have the time (and $$$) then MR is a good option.