IPhone 3GS headphone sound is crackly

(posted as an answer so you can accept it and mark this issue resolved)

Have you checked the Sound pref pane in System Preferences? There's a tab labeled "Output" where (I'd expect, as I don't have a portable in front of me just now) you can switch output between built-in speakers and the headphone jack. If the first toggle doesn't work, toggle it again.

I had this issue with my iPhone 4. Turns out some debris got in the headphone jack. As the 3GS is an older device, the contacts may be dirty.

Try taking a cotton swab with most of the cotton removed and dipping it in rubbing alcohol. While it's off, clean the sides of the headphone port on the 3GS.

Let it sit for five minutes and turn it on. See if that helps.

Another thing you can do is quickly and forcefully insert and remove the headphones in question to (hopefully) clear anything blocking the contacts.

Personally, I'd try the first option first.