I usually use set_time_limit(30) within the main loop (so each loop iteration is limited to 30 seconds rather than the whole script).
I do this in multiple database update scripts, which routinely take several minutes to complete but less than a second for each iteration - keeping the 30 second limit means the script won't get stuck in an infinite loop if I am stupid enough to create one.
I must admit that my choice of 30 seconds for the limit is somewhat arbitrary - my scripts could actually get away with 2 seconds instead, but I feel more comfortable with 30 seconds given the actual application - of course you could use whatever value you feel is suitable.
Hope this helps!