Is it possible to show ongoing notifications under regular notifications? On my Galaxy S3 (4.0.4) when I drag the notifications bar down to see the list of the notifications, the ongoing ones (e.g. wifi) are always on the top and the regular ones (e.g. gmail) are the at the bottom.

That seems reversed. It means to see a recent notification that just beeped a user has to drag the bar down and then scroll down.

Is there any way to reverse them so the recent/non-ongoing ones are on top? Either in 4.0, or perhaps something i can look forward to in 4.1, or perhaps in cyanogenmod (I will switch to eventually).
Notifications, at least in CyanogenMod or AOSP, are ordered in order or the last updated notification.

If you have an app that updates the notification, then the notification will appear on top when it updates.

There is currently no way to change this behaviour.

Note: Some stock ROMs order the notifications into ongoing etc, this is the design of the manufacturer, and can also not be changed 

You should get something like what you are asking in cyanogenmod.