The difficulty is not in saving the file with a different extension, since you could always rename it in Explorer anyway.
The difficulty lies in inserting arbitrary binary data into the file. Notepad is a text editor and i'ts not easy to use it for placing any bytes you want into a file.
In any case, programming in binary is not really a good idea, unless you think servicing your car with a fish is a good idea. Or writing an accounting package in BCPL, or an operating system in COBOL, or anything in Pascal :-)
Yes, we had to do it by flipping toggle switches in the early days of the PC world but I think you'll find it a lot easier to pick up one of the free assemblers (nasm, yasm, gas, etc) and program in assembly language. You can do that in Notepad quite easily, and then pass it through the assembler of choice to produce an executable.