For example, if I have a cut of beef or salmon, and I want to sous-vide cook either unpasteurized (rare or medium-rare) or pasteurized (medium+), based on thickness and temperature, how long should I cook each for?
The best resource I know of for sous vide pasteurization times is Douglas Baldwin's A Practical Guide to Sous Vide Cooking.
The recipes section has tables for pasteurization time as a function of temperature and thickness for fish, poultry, and red meat. Note that for red meat, there are pasteurization times down to 131F/55C, which is generally regarded as medium-rare, so you have the matchup between pasteurization and doneness slightly off.
In the basic technique/cooking section, there are also tables for heating times, starting from either refrigerator temperature (41F/5C) or frozen (0F/-18C), going to 1F/1C short of the water bath temperature, for various shapes of meat.
If you're aiming for pasteurization, you want to use both tables, to make sure that the meat is both pasteurized and heated through. You'll also be fine cooking for longer than that, since it's safely pasteurized.
If you're cooking something rare enough that it won't pasteurize, you can just use the heating times table. In that case, you'll want to try not to cook too much longer than the given time, since it's not getting any safer.