In countries with negative short-term risk-free interest rates, do you just use a negative "r" in the Black-Scholes formula, or do adjustments need to be made?
The Black Scholes world does not assume $r>0$. So, you can just plug in a negative number for $r$. Note that the lower $r$, the lower a call option price.
The only assumption regarding interest rates is that they are constant during the lifetime of the option.
It is possible though to generalise the model and allow for time-dependent or random interest rate (e.g. hull white model or shifted CIR model). This can provide a more accurate incorporation of interest rates.
Of course, other caveats remain and the Black Scholes setting is very simplistic and fails to capture real world price dynamics. One ought to be careful to apply it in real world.