The Default Clinical Pipeline produces the most commonly desired output from cTAKES.  
This includes annotations for Anatomical sites, Signs/Symptoms,
Procedures, Diseases/Disorders and Medications.
For each annotation there are normalized UMLS CUIs, plus values for negation, uncertainty and subject.  
The Default ClinicalPipeline is a great place for the new user of a binary installation to start.
New developers should look at the ctakes-examples project to start.