...beyond the tutorials two suggestions for file 'upload' to the board:
1. Modify our 'web_server' example to support HTTP POST. Actually, it does support POST, but just prints out a silly message to demonstrate it. You'd need to add the additional code to figure out that a file was coming to malloc space for the file, and then to receive it via the sockets interface. This is probably documented/exampled in other open-source web server software out there.
2. Find the compact-flash example designs from our partner Microtronix. There is a compact-flash component that covers the hardware. I am not sure if there is file-system-read support in this, but its worth a look. This way you could copy files to CF and then copy them into Nios memory.