Whisk together the soy sauce, brown sugar, water, garlic, onion, ginger, black pepper, oregano, red pepper flakes, cayenne pepper, and paprika in a large glass or ceramic bowl. Add the chicken thighs, and toss to evenly coat. Cover the bowl with plastic wrap, and marinate the chicken in the refrigerator for at least 1 hour.
Preheat an outdoor grill for medium heat, and lightly oil the grate.
Remove the chicken thighs from the marinade. Boil the remaining marinade until reduced to a syrupy consistency. Grill the chicken thighs on the preheated grill until cooked through, about 15 minutes per side. Glaze the grilled chicken with the marinade sauce or serve the marinade on the sideas a dipping sauce.