Several ways to do it:
Easiest is ftp. You could also use a null-modem serial cable and a terminal emulator at each end. You could also burn the data to CD on either machine, to be read by the other. If you have Frying Pan for the Amiga, you could do the same with DVD. Note that you do not need Frying Pan to read DVDs on the Amiga, but you do need it to write them. If you're talking small files, just use CrossDOS. Its also possible to set up NFS shares, or even parallel links. If you have an A1200, there are PCMCIA flash cards you can use. If your Amiga has USB, there are yet many, many other ways it can be done.