In a bowl toss together diced onions and salt and let set at room temperature for about 10-20 minutes.
In a skillet heat oil and add the diced onions with any liquid that has macerated. Cook over medium high heat until translucent, stirring occasionally, about 10-20 minutes.
Add black pepper and thyme to onions. Lower heat to medium low.
Add balsamic vinegar and honey to onions and cook for about 20 minutes, stirring frequently.
After about 20 minutes increase heat and cook until thick and a jam like texture. Stir frequently as to not let mixture stick or burn to pan.
Can be eaten right away or stored in an airtight container in refrigerator, up to two weeks. Is great on sandwiches, toast, salads, meats, vegetables, etc.