I currently have a 2006 Cannondale Prophet 1000, that I use for trail riding. I would like to upgrade the Manitou Swinger rear shock I have. How do I know which shocks will work with my bike? Is there a guide to choosing a shock that will fit best?
Any shock with an eye to eye length of 20.0 cm (7.9 in) and 5.0cm (2.0in) stroke will fit as a direct replacement for your shock. All the shocks available as OEM options on the 2005 Prohphet used these dimensions.
Any different eye to eye length will alter the geometry of your bike. Any different stroke length will either reduce travel, or if risk damaging your frame if the travel is too long.
As to setup, that will depend on your weight and riding style. I will add that the prophet is a single pivot design, so you may benefit from platform technology to prevent bobbing.
You will also need to make sure the eye-to-eye length is same as your current shock (that's the distance from the centre of the pivot hole in one end to the pivot centre in the other), and that the stroke length is the same. If either of these is wrong, it will change your bikes geometry and possibly even cause the rear tyre to bottom out against the seat tube.
Is there a guide to choosing a shock that will fit best?
If only it was that simple. Different shocks behave differently on different frames with different air pressures/spring rates - it would be impossible to make a complete guide. Not to mention that how the bike feels to you is unquantifiable.
It may be better to further expand your question to say why you don't like your current shock, and why you think changing it would make your bike feel better. It may just need to be sent away for a servicing.