I have found the answer to winterboard slowing down the iphone.
Add the,
Http://david.ashman.com/apt/ repository to Cydia.
Then add the winterboard settings from this repository. It moves the winterboard settings into the system settings app. Within the new winterboard settings select the springboard only slider and hit the home button and the phone will respring and then I rebooted just for anality. The apps are now fast initializing and shutting down!
Also if your interested...
In that repository is an updated weather icon for the stock weather app. If installed along with Supreme Preferences, and the Katra or Klear weather icons you will have an updating weather icon. Note it will use the weather from the first page of the weather app.
Note: Supreme Preferences when selected within Winterboard changes the stock settings icon and adds a setting menu for itself in the settings app adding some configuration for weather icon and other nice features.
Keep an eye on David Ashman,
weathericon - Google Code
Peace,
Cy