The most common known education organizations for learning functional medicine.
The IFM is probably considered the "Mothership" organization, with modules heavily focused on the science. When CME is involved, protocols and specific labs/supplement companies are not able to be included in individual presentations. Question and answer sessions (in person and online) are set up to address more specifics. Kresser's ADAPT course is newer, and he does mention protocols and specific labs/supplements.
Courses with a focus on nutrition and labs associated with nutrition. I've heard a lot of good things about Holistic Nutrition Lab (supposedly very detailed, which I appreciate). Kripalu specifies that it is for nurses and nurse practitioners, but I don't know if other professions can take the courses.
Organizations that are maybe lesser known, but offer certifications/degrees as a part of comprehensive programs.
Courses that focus on practitioner mentorship in addition to teaching principles of functional/integrative medicine. Dr. Kalish recently partnered with IFM to provide business coaching for those interested in starting a functional medicine practice (talks on this subject are not part of CME credit, and usually occur in the evening). Chris Kresser's course would also fall under his category. You can learn more about Freedom Practice Coaching via podcasts from the Functional Forum.
Courses offered through lab or supplement companies.
Apex is not free, but is very detailed and focused on biochemistry - they often offer a discount for the first course you take.
Other links are to videos or handouts particular to specific labs (all free).
Health Coaching educational resources.
Courses that focus on specific topics, such as ancestral health, genetics, lifestyle medicine, health coaching, and more.
Resources that aren't training courses per say, but that have good inspirational information.