Assuming pure Windows (i.e., no Cygwin, et al.) and that you don't want to or can't install anything to do it with, I'd suggest using a Visual Basic script to do the job. You might try something like:
targetDir = WScript.Arguments.Item(0)
WScript.Echo "Operating on files in " + targetDir
Set fsh = CreateObject("Scripting.FileSystemObject")
Set targetFiles = fsh.GetFolder(targetDir).Files
ZeroPadWidth = Len(targetFiles.Count)
FileNumber = 0
For Each File In targetFiles
FileNumber = FileNumber + 1
NewName = targetDir & "\"
For I = 1 To ZeroPadWidth - Len(FileNumber)
NewName = NewName & "0"
NewName = NewName & FileNumber
WScript.Echo "Renaming " & targetDir & "\" & File.Name & ": " & NewName
Put that into a file, e.g. "rename.vbs"; then, call it from the command line, with the target directory as the sole argument, like this:
c:\Users\Username\Desktop> cscript rename.vbs "c:\target\directory"
It will produce filenames which are ordered numerically and left-padded with zeroes; if you have a directory with a thousand files in it, you'll get names ranging from 0001, 0002...0999, 1000.
No warranty, but it should do what you need. If it doesn't, let me know. (And make a safe copy of the target directory just in case; I've tested this a bit, and it should be OK, but there's always the possibility of the bug I didn't catch.)
Hope this helps! (If it does, I hope you'll take Shinrai's point about accept rates to heart.)