Either type of scanner works well with filemaker. Here where I work, we scan the mag strips of CA Driver's licenses to capture name, address, and other data encoded on the back.
Almost all of these scanners operate in keyboard emulation mode which means your computer perceives the input from the scanner just as though you typed the data in from the keyboard. Thus, in it's most basic format, you'd just place the cursor in the right field and scan the card.
To enhance the process, most scanners can be programmed to put characters at the beginning and ends of the scans. You can use OnKeystroke script triggers to respond to these special characters to put the cursor in the correct field and then process the result.
With versions of filemaker older than 10, you can pause the script in an infinite loop and use an enter key "post-amble" to trigger the loop to continue with each successive scan.