Quasar Cydia tweak is the very first window manager for iPad that allows you to run apps in windows. When you open an application it will be opened in a window, just like on your computer. “Quasar is fully integrated to default app switcher, if you kill an application from the app switcher it will kill its window and the application, but if you click the close button, only the window will close and the application will continue to run in the background.“
However, Quasar does not come cheap. You can get it via the BigBoss repo for $9.99 and you need iOS 5 or higher to use this tweak.