Loose body within a Baker's cyst: The presence of a 2.9 cm long body at the popliteal fossa, possibly within a Baker's cyst, along with moderate tricompartmental osteoarthritis, strongly suggests that the loose body is related to the osteoarthritis and is likely located within a Baker's cyst.

Primary synovial chondromatosis: This condition involves the growth of cartilage in the synovium, which can break off and form loose bodies. The presence of multiple loose bodies, as suggested by the mention of a "more subtle smaller body just inferior," could indicate this diagnosis.
Osteochondritis dissecans: Although less likely given the description, osteochondritis dissecans could result in a loose body within the knee joint, especially if there's a history of trauma or repetitive stress.

Popliteal artery aneurysm or other vascular anomaly: Although the description points towards a loose body within a Baker's cyst, it's crucial not to miss a vascular anomaly, such as a popliteal artery aneurysm, which could present as a mass in the popliteal fossa and has significant implications for patient management and outcome.
Soft tissue tumor (e.g., synovial sarcoma): While rare, a soft tissue tumor could present as a mass in the popliteal fossa and must be considered to ensure timely diagnosis and treatment.

Intra-articular osteoid osteoma: This benign bone tumor could potentially cause joint symptoms and loose bodies, although it's a less common cause of such findings.
Synovial hemangioma: A vascular tumor of the synovium, which could present with joint symptoms and possibly loose bodies, although it's rare and not typically the first consideration in this clinical context.