The windows application should manage files, in the way that if I select a folder to be synced, it should sync automatically. When a transfer is interrupted, it continues next time I turn on the PC. If a folder is synced, when I change a file it should automatically update it in the servers.. and if I upload a file to the web interface in a synced folder, it should download automatically in my PC. That should work also on shared folders, so that many can work on the same file.

Have an option to limit the bandwith used for downloads or uploads in the windows app

I think it's better to have a small icon in the system's tray in order to save taskbar's space for oder programs. Maybe when you place the mouse over it, show the upload/download rate, and pop up messages when transfers are done. Right click should pop up options.

Great for backups. Sync the files between the computer and aruna.

Users will greatly benefit from having a 'Compare' command in the client software, which compares contents of the two panes based on file names and timestamps and in each pane highlights files that are newer than those in the other pane, and those that are missing from the other pane. This would facilitate very easy way to synchronize contents of folders while keeping full control with the user (the user may deselect some files before uploading).