You can't change the boot drive letter with out doing some serious hacking and yes it may cause programs not to run. If you just want to change drive letters like your cd-roms drive letter or another partition that you have created like a storage partition then you shouldn't have any problems.
To change drive letters go to control panel--> administrative tools (you may need to switch to classic view)--> computer management--> expand storage--> click on disk management--> right click on the drive you want to change (it should go from white to white with diagnal stripes)--> choose change drive letter and paths.