The Schematic Design Tool I use is Altium Designer. I also have older versions of Pcad 200x, OrCad SDT and Viewlogic Workview. I use the OrCad for modification to existing designs and the Viewlogic Workview is for modifications to early Xilinx FPGA designs.
Each part placed on the schematic includes attributes which help in generating an accurate BOM listing. This listing is then imported into an Excel spreadsheet.
"MFG#" Component Manufacture Part Number
Once the schematic and BOM are complete, a netlist can be compiled which will import directly into Pcad PCB layout.