Citrus used to allow multiple copies of itself to be run, which was bad. Now it just gives a message that it's already running, which is better. However, the optimal behavior is to maximize the app from the system tray.
Rationale: for anyone that's using windows 7 and/or keyboard launcher (e.g. Launchy), it's generally easier to hit "start" and type "citrus" than to fish for an icon that's probably hidden in the system tray on a (possibly hidden) taskbar. I'm using Citrus a.c. now, but I'd be tempted to switch to an alarm clock app that implements this behavior.