Android - Linux program to transfer file from/to an android device?

There's QtADB which uses adb.

You can also install an SSH or ftp server on the phone and then use Nautilus with ssh://ip-or-name-of-your-phone/ or ftp://ip-or-name-of-your-phone/ URLs (you can create bookmarks in Nautilus). The cool thing about a standard SSH or ftp server on your phone is that you don't have to install anything special on the computer.

I use QuickSSHd on the phone, but there are also other SSH servers available (search the market, please).

Ftp servers I know are SwiFTP and FTPServer. I didn't test these with Nautilus yet, but they should work.

If you install Eclipse with the Android SDK there is a perspective called DDMS that includes a file explorer. You can easily copy files from/to the device with this tool, which uses adb push/pull in background.

Another way is to simply unmount the SD card from the phone and use it as a mass storage. But in this mode you can access only the SD card and the debug mode must be disabled which can be annoying if you need the device to stay in debug mode for development.