In the Clock app, if I use a timer or alarm that goes off while my iPhone is on vibrate mode, the alarm sound still goes off. Is there a way to make it obey the vibrate mode? Or a way to tell it whether or not to ignore it?
Calendar alarms obey the mute switch. Clock alarms do not.
Personally, I consider this a feature and not a bug--but I can understand why you'd at least want the option.
However, short of jailbreaking, there is currently no way to change this behavior in the Apple-provided applications.
Create a silent ringtone (e.g. a short piece of silence in Garage Band or the ringtone creator of your choice) and set that as the sound for the alarm.