The basic controls in WinXP or 98Se allow you to individually set the relative position of the monitors (how the mouse moves from one to the other) and the resolution and frequency of the monitors. This is really all I use in my dual monitor setup.
However I have an ATI dual monitor card (Radeon VE) which includes the Hydravision software that has many other options. These allow you to store multiple desktop configurations, control where dialog boxes pop up, control whether the applications always start at the same place or start where they were closed, etc. All this seems very handy but I've never had a need to use it.
I think there are third party applications to do the same things on a two video card setup. However, the dual monitor AGP cards are very slick way to get there and the cost is surprisingly low.