The web interface allows more fine-tuned administration of the unit. The QNAP Finder more-or-less is just a tool to help those who aren't as comfortable with web interfaces administer the basic functions of the unit and map drives on the local computer.
The TS-109 can connect to Windows Active Directory, as well as serve up AFP, FTP, and NFS shares. It can also act as a DHCP and SSH server.
One can also configure the eSATA and USB ports to act in RAID 1 or independently. Unfortunately, the filesystem options are limited to FAT and EXT3, so those with NTFS drives will have to reformat in order to use them read/write. It can also be used in conjunction with a USB UPS.
One can configure users and groups on the device, and set up replication with a remote host or even onto a local drive. It also has a pretty detailed log.