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if I'm not mistaken you delete them as you normaly would a reular app from app store just click and hold till it starts jiggling then hit the x.

And if I'm wrong then I hope some answers your question better
 
@ Acronym,
You are mistaking. ;)

@ bath007,
Launch Cydia and go to Manage > Packages > Select the app you wish to get rid of > Modify > Remove.
 
You have to go back into Cydia and select "manage packages" on the menu, from their you can uninstall any package you may have installed.
 
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