The basic breakdown:
New Pathway: PBL, focuses on social issues, more students
HST: joint program with MIT, extra req's (differential eqn's and calc-based phys), lectures/semester format, focuses on science, more difficult, supposedly students receive more financial aide, thesis required and many students stay a fifth year for it, many others join the MD/PhD program
Scanned straight from MSAR:
The New Pathway Program is designed to accommodate the variety of interests, educational backgrounds, and career goals that characterize the student body. Basic science and clinical content are interwoven throughout the four years. In the first and second years, a problem-based approach that emphasizeds small-group tutorials and self-directed learning is complemented by laboratories, conferences, and lectures. Students are expected to analyze problems, locate relevant material in library and computer-based resources, and develop habits of lifelong learning and independent study. Clinical clerkships and a wide variety of elective courses and research opportunities are available at Harvard Medical School, its affiliated hospitals, Harvard University, and the Massachusetts Institute of Technology (M.I.T.). One hundred thirty-five students are admitted to this program each year.
A second M.D. pathway is the Harvard-M.I.T. Division of Health Sciences and Technology Program (HST). This program was established jointly by the faculties of these two institutions. The curriculum of this program is designed for the student with a strong interest and background in quantitative science. Courses in the first two years are taught both at Harvard Medical School and M.I.T. with faculty drawn from both institutions. The curriculum is in a semester format. HST students join studnets of the New Pathway Program for their clinical rotations. A thesis is required for graduation. Thirty students are admitted to this program each year.