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What I'd like to do is to create an interrupt one a timer expires after 1 ms ... 100 ms. It doesn't even have to be very accurate.

Working with microcontrollers I'm used to start a timer say in main() and get an interrupt when it expires.

But how do I set this up with the Raspberry Pi? I'm using WiringPi but so far I haven't found how to do this.

I'd be happy to get some insights on this. Thank you very much.

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The wiringPi library provides a number of blocking timer calls. One is used for micro second granularity (delayMicroseconds) and the other is used for milli second granularity (delay). See:

http://wiringpi.com/reference/timing/

Using either of these, you can block your C program for a configurable amount of time. For example, if you need to send a pulse every 50 milli seconds, you could code:

while(1)
{
   // Code to send a pulse
   delay(50);
}

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