The way that I've found that works for me, is to create my checkboxes as an array:
<input type="checkbox" name="cb[1]" value="1">
Then in my scripts I use a while loop to walk through each value in the array and do some processing on it. Since if the box isn't checked it won't be passed to the next script you need to verifiy that it exists, it's easier to check this with an array than a bunch of uniquely named values.