There's an issue with user alerts not functioning in one site collection (on SharePoint 2010). Apparently, the alerts were working and somewhere down the line they stopped. I couldn't find out exactly when this issue started occuring.
When creating an alert (on a list/library/etc), an e-mail does get sent, however, there are not any other alert e-mails. I've created workflows which send an e-mail and these work fine.
I've checked the timer jobs and there are not any issues with the timer jobs, according to Central Administration.