What meats can I serve medium rare and why?

Beef (and Lamb): The surface of beef is often contaminated with pathogens such as e-coli. However, the meat is very dense and the bacteria cannot migrate from the surface into the flesh. Therefore, beef is safe to consume once the external temperature exceeds, 160 degrees F. The internal uncontaminated meat is safe to eat raw.

Pork: Like beef the surface of pork needs to be fully cooked. Unlike beef, pigs harbor a parasitic roundworm called Trichinella spiralis. Infection with the worm is called trichinosis and can be fatal. This worm is killed when the flesh reaches 150 degrees F and is held there for several minutes. Therefore pork is safe to consume when cooked to medium. (Commercial pork in North America almost never has the roundworm present. Almost every case (all?) of trichinosis in the last 15-20 years have come from undercooked wild boar or bear meat). Trichinella spiralis can also be killed by freezing (time and temperature dependent).

Chicken: Almost all chickens have Salmonella or Campylobacter present on the surface (at least). However, chickens have a less dense flesh than pigs, sheep or cows. Therefore, the bacteria can migrate deep into the flesh. Also, the processing of chickens is much more invasive than the previously mentioned animals which also means the interior meat can get contaminated. This means the meat must be cooked to well done throughout.

Duck: With duck it seems to come down to a matter of processing verses chicken. Also, they are raised in a much less confined manor, which helps prevent the spread of pathogens. There is still a chance of getting a salmonella infection from undercooked duck but cooking the breast well done basically ruins it, so people take the (small) risk.

Ground meat: Grinding meat, by its nature, implies the surface and the interior is mixed. Therefore, one must assume the meat is fully contaminated and must be entirely cooked to well done.

Chicken meat and eggs carry the risk of salmonella. Salmonella are bacteria which cause severe symptoms, and can even end in death, unlike other, milder types of food poisoning. They are also hardy bacteria, and the temperature needed for them to die quickly is above the temperature for medium rare. In theory, you could eat poultry medium rare if you ensure that it has stayed at the lower temperature for a sufficiently long time, but the relationship is not linear, and if you are not well acquainted with the times needed and don't use a thermometer consequently, it is safer to heat it to well done.

Pork is known as a possible source of trichinosis, which is caused by a parasite. It also needs very high temperatures to die. Systematic veterinary control has almost eradicated trichinosis in developed countries for commercial pork, so eating pork at medium rare is considered reasonably safe today. Care should still be taken if you are preparing wild boar as a significant risk of trichinosis remains in game hogs. (Small slaughter houses and butcher shops may offer pork from wild boars in (following) hunting season.)

Other meats have their own share of nasties, especially E.coli - they are usually just unpleasant, but some strains can be very dangerous, like the one in Germany last summer. Be warned that with modern safety procedures, you are more likely to get your food poisoning from produce (because it is often not heated, but eaten as salads, etc.) than from meat. So don't forget to wash your veggies.

You can serve almost any protein medium rare. I wouldn't want to eat poultry at that temperature, mind you.

Cooking the protein to high temperature is not the only way to cook it safely. The high temperature kills almost all of the bacteria in seconds. But a lower temperature for a longer period of time does just as well.

For instance, this chart lists how long it takes to pasteurize (kill the bacteria and other organisms) some common protein.

From http://www.douglasbaldwin.com/sous-vide.html#Table_5.1 -

Pasteurization Time for Meat (Beef, Pork, and Lamb)
(starting at 41°F / 5°C and put in a 131–151°F / 55–66°C water bath)
55°C    56°C    57°C    58°C    59°C    60°C
Thickness   131°F   133°F   134.5°F 136.5°F 138°F   140°F
5 mm    2 hr    1¼ hr   60 min  45 min  40 min  30 min
10 mm   2 hr    1½ hr   1¼ hr   55 min  45 min  40 min
15 mm   2¼ hr   1¾ hr   1½ hr   1¼ hr   60 min  55 min
20 mm   2½ hr   2 hr    1¾ hr   1½ hr   1¼ hr   1¼ hr
25 mm   2¾ hr   2¼ hr   2 hr    1¾ hr   1½ hr   1½ hr
30 mm   3 hr    2½ hr   2 hr    2 hr    1¾ hr   1½ hr
35 mm   3¼ hr   2¾ hr   2¼ hr   2 hr    2 hr    1¾ hr
40 mm   3½ hr   3 hr    2½ hr   2¼ hr   2¼ hr   2 hr
45 mm   4 hr    3¼ hr   3 hr    2¾ hr   2½ hr   2¼ hr
50 mm   4½ hr   3¾ hr   3¼ hr   3 hr    2¾ hr   2½ hr
55 mm   5 hr    4¼ hr   3¾ hr   3½ hr   3 hr    3 hr
60 mm   5¼ hr   4¾ hr   4¼ hr   3¾ hr   3½ hr   3¼ hr
65 mm   6 hr    5¼ hr   4¾ hr   4¼ hr   4 hr    3¾ hr
70 mm   6½ hr   5¾ hr   5¼ hr   4¾ hr   4¼ hr   4 hr

61°C    62°C    63°C    64°C    65°C    66°C
Thickness   142°F   143.5°F 145.5°F 147°F   149°F   151°F
5 mm    25 min  25 min  18 min  16 min  14 min  13 min
10 mm   35 min  30 min  30 min  25 min  25 min  25 min
15 mm   50 min  45 min  40 min  40 min  35 min  35 min
20 mm   60 min  55 min  55 min  50 min  45 min  45 min
25 mm   1¼ hr   1¼ hr   1¼ hr   60 min  55 min  55 min
30 mm   1½ hr   1½ hr   1¼ hr   1¼ hr   1¼ hr   1¼ hr
35 mm   1¾ hr   1½ hr   1½ hr   1½ hr   1¼ hr   1¼ hr
40 mm   1¾ hr   1¾ hr   1¾ hr   1½ hr   1½ hr   1½ hr
45 mm   2¼ hr   2 hr    2 hr    1¾ hr   1¾ hr   1¾ hr
50 mm   2½ hr   2¼ hr   2¼ hr   2 hr    2 hr    2 hr
55 mm   2¾ hr   2¾ hr   2½ hr   2½ hr   2¼ hr   2¼ hr
60 mm   3 hr    3 hr    2¾ hr   2¾ hr   2½ hr   2½ hr
65 mm   3½ hr   3¼ hr   3¼ hr   3 hr    3 hr    2¾ hr
70 mm   3¾ hr   3¾ hr   3½ hr   3¼ hr   3¼ hr   3¼ hr

Table 5.1: Time required to reduce Listeria by at least a million to one, Salmonella by at least three million to one, and E. coli by at least a hundred thousand to one in thawed meat starting at 41°F (5°C). I calculated the D- and z-values using linear regression from O’Bryan et al. (2006), Bolton et al. (2000), and Hansen and Knøchel (1996): for E. coli I use D554.87 = 19.35 min; for Salmonella I use D557.58 = 13.18 min; and for Listeria I use D559.22 = 12.66 min. For my calculations I used a thermal diffusivity of 1.11×10-7 m2/s, a surface heat transfer coefficient of 95 W/m2-K, and took ?=0 up to 30 mm and ?=0.28 above 30 mm (to simulate the heating speed of a 2:3:5 box). For more information on calculating log reductions, see Appendix A. [Note that if the beef is seasoned using a sauce or marinate which will acidify the beef, then the pasteurizing times may need to be doubled to accommodate the increased thermal tolerance of Listeria (Hansen and Knøchel, 1996).]

There is more of this information available. Look for sous vide cooking times to see the appropriate cooking time for you choice of protein.

Traditionally pork and chicken have been more disease ridden, carriers of parasites, and have high surface bacteria counts. So thorough cooking has always been advised

If you know the source of the pork or chicken, you can cook it rare too. Some cultures will eat it raw

It all comes down to how much you know and trust your meat provider

There are also doggy beef and lamb suppliers out there, that you would be best to thoroughly cook beef and lamb from them too