MeGrowTall,
I've recently put together a website [link on the bottom] with information on NIGMS-funded and non-NIGMS funded MD/PhD programs. I think the best judge of a programs strengths and weaknesses can be better stated by speaking with the director of the program, and especially some students who are in the program. Ask them what sort of things they do - ie retreats, research presentation get-togethers, clinical training during the PhD years, etc. Ask specifically about what sort of funding they provide for you through your MD and PhD years; IMHO, you shouldn't saddle yourself with $200,000 in debt if you plan a career in comparatively low-paying research.
I'd also say that an up-to-date website with lots of information, listing of students, FAQs, and research strengths is also the sign of a strong program

.
While in most cases you can't go badly with an NIH-funded MSTP, non-funded programs CAN and ARE good, it just matters what you want, who is there that you're interested in working with, and what sort of benefits and activities the program has. I'd say right now is about the right time to start putting out feelers.
Best of luck,
Jason