Why should I choose 36 or 32 spokes (or another number)? I have to change the rims of my bike and I have to choose between 32 or 36 (or 48 or any other variation). I never thought about this until now and I feel it's kind of a dumb question, but I don't have a clue if this has any perceptible impact or not.

So far, I understand that more spokes means a stronger wheel, but also more spokes means a little bit more weight. Despite that, a spoke weights almost nothing so I think that's not a practical difference to take into account.

Is there anything else? I ride a single speed bike mainly for city commuting, so is there any practical difference between choosing 32/36 spokes (or another number)?

Thanks a lot people!
Lower spoke numbers are primarily of interest to weight weenies (though for a given price, a lower spoke wheel will probably use a heavier rim offsetting the spoke reduction weight savings). 

As usual, Sheldon is some good reading. There is also a whole book on how to build wheels well and design decisions, by Jobst Brandt, called "The Bicycle Wheel".

What matters for most people is using a good amount of spokes, good spokes, a good rim and hub, and putting them together well (and how they're put together) - pretty much any wheel is going to be bad if the wheelbuilder messes up/sucks. 

Heavier riders often should go with a higher spoke number than a lower spoke number and tougher rims+spokes. According to Sheldon, it used to be that you'd run 36 front, 36 back then we started dropping. On a commuter, I'd emphasize durability, so I'd probably go with the more spoke option.

The best thing to do is talk to a good wheel builder and assess your individual needs. If you got to the point where rim wear was what made you replace the rim, chances are you're fine with whatever you had. If you're replacing the rim, make sure to use new spokes and make sure the hub is in good condition.