Specifically, I'm interested in flashing a leaked build of Ice Cream Sandwich on my Nexus S 4G. I'd like to get in on the action early, but this is something I'd like to know.
If you are installing a custom ROM that is not a "carrier leak" then you probably will no longer receive OTA notifications/updates.
In the custom ROMs they remove the OTA settings that the carriers use. I don't know exactly what is changed/removed, but I can't even tell you the last time I have had an OTA notification.
But if you use tools like ClockWorkMod Rom Manager you can get notifications for updates to the ROM you install if it is added to Rom Manager by the developers. This is how I get my update notifications for CyanogenMod.