Well, I know the shell script would need POSIX paths to the files, but it probably won't receive them that way; I think you'd have to send the paths through an AppleScript to convert them, and at that point, you could just run the shell script from inside the AppleScript too.

After your files are choose:

Applescript:

on run {input, parameters}
set command to "/Users/dara/Web/bin/pdfcombine\\ Folder/pdfcombine "

repeat with thisItem in input
set command to command & quoted form of POSIX path of thisItem & space
end repeat

do shell script command & "-o final.pdf"
end run

Edit: Actually, the shell script does receive a list of POSIX paths. I'll try something else then… (FYI: http://developer.mabwebdesign.com/pdfcombine.html)

Edit: It doesn't use stdin…


Edit: Ok, use this shell script after you select the files:
[code]/Users/dara/Web/bin/pdfcombine\ Folder/pdfcombine "$@" -o /path/to/final.pdf[/code]
You should pass input as arguments (that's the "$@").