IMHO, the best way to apply trapping is to do it when ripping, when it is possible. This way, the trapping is only applied when needed and with correct values. But if you want to do it in Illustrator, it's quite possible.
The method explained in the link posted by arkay_desai works well and can also be used to overprinted thin stokes added to shapes. But there is also a more powerful function hidden in Effects>Pathfinder>Trapping (sorry if this path is not right but I only have a french version of Illustrator). First you have to group all the elements on which you want to apply the trapping. Then you go to Effects>Pathfinder>Trapping and you adjust the parameters according to your needs. The trapping is only made where it is necessary and the results is automatically modified if you move or transform an object (it's an effect and not a filter).
There is also another solution with InDesign. If you want, you may import the .ai file (it doesn't work with eps anymore) in an InDesign page and create a PDF using the print function (it's not possible with Export). This method is explained in
an article posted on InDesignSecrets.com. It uses a powerful trapping engine inside InDesign. If you want to see the result, don't forget to activate the overprint preview in Acrobat. Otherwise, it can be ugly.
