Is there any particular reason to prefer one of these filter designs over the other? Theoretically, they are the same. Practically, does changing the order of the resistor and capacitor have any effect (except, perhaps, on physical layout)?
Answer
Yes, in certain circumstances there is a difference between the two.
Consider the case where the amplifier operates in large electric fields, and the impedances are high (e.g. megohms). Then, every millimetre of wire or PCB track between the highest impedance components and the "virtual earth" (negative input) is an antenna picking up noise.
So place the highest impedance component adjacent to the opamp and the lower impedance one further out to minimise the area and minimise interference.
Then you have to ask which of R1 and C1 is the higher impedance component... I can't answer that without knowing the context; but a couple of examples may help.
1) Lots of low frequency interference at say 50 or 60Hz: comparing R and Xc you probably find the capacitor is the high impedance component, and the resistor placement is less critical.
2) High frequency interference (e.g. in a switch mode power supply or RF transmitter) . Xc is small, and R is the high impedance component.
3) Special case of 2) The amplifier has a lot of gain at HF and tends to form an unintended UHF oscillator : introduce a new resistor between the circuit node and -Vin, as close to -Vin as possible. This resistor is small (a few hundred ohms maybe) and is known as a base stopper (or grid stopper, or gate stopper, depending on the amplifier!)
But there are many cases where it simply doesn't matter.
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