Use Transmission-daemon on a headless Ubuntu server for remote control the torrents. Here I installed Transmisiion-daemon in a headless server running Ubuntu.

Transmission is a fast, simple and cross-platform free BitTorrent client,  feature spotlight are,

• Uses fewer resources than other clients
• Native Mac, GTK+ and Qt GUI clients
• Daemon ideal for servers, embedded systems, and headless use
• All these can be remote controlled by Web and Terminal clients
• Bluetack (PeerGuardian) blocklists with automatic updates
• Full encryption, DHT, PEX and Magnet Link support

Check new release at www.transmissionbt.com.

Installation(Ubuntu)
$ sudo apt-get install transmission-cli transmission-common transmission-daemon

Start and stop Daemon
$ sudo /etc/init.d/transmission-daemon start (stop)

Edit Configuration Settings

First, stop the daemon before editing.

$ sudo nano /etc/transmossion-daemon/settings.json

Some options(ref to WIKI):

• download-dir: String
• incomplete-dir: String (directory to keep incomplete files in)
• incomplete-dir-enabled: Boolean (default = false) When enabled, new torrents will download the files to incomplete-dir. When complete, the files will be moved to download-dir.
• watch-dir: String
• watch-dir-enabled: Boolean (default = false)

• rpc-authentication-required: Boolean (default = false)
• rpc-bind-address: String (default = “0.0.0.0″) Where to listen for RPC connections
• rpc-enabled: Boolean (default = true)
• rpc-password: String
• rpc-port: Number (default = 9091)
• rpc-username: String
• rpc-whitelist: String (Comma-delimited list of IP addresses. Wildcards allowed using ‘*’. Example: “127.0.0.*,192.168.*.*”, Default: “127.0.0.1″ )
• rpc-whitelist-enabled: Boolean (default = true)

My sample setting file for example:
{
“blocklist-enabled”: 0,
“download-dir”: “\/home\/user\/downloads”,
“incomplete-dir”: “\/home\/user\/tpm”,
“incomplete-dir-enabled”: 1,
“download-limit”: 100,
“download-limit-enabled”: 0,
“encryption”: 1,
“lazy-bitfield-enabled”: 1,
“message-level”: 2,
“open-file-limit”: 32,
“peer-limit-global”: 240,
“peer-limit-per-torrent”: 60,
“peer-port”: 51413,
“peer-port-random-enabled”: 0,
“peer-port-random-high”: 65535,
“peer-port-random-low”: 1024,
“peer-socket-tos”: 0,
“pex-enabled”: 1,
“port-forwarding-enabled”: 1,
“preallocation”: 1,
“proxy”: “”,
“proxy-auth-enabled”: 0,
“proxy-auth-password”: “”,
“proxy-auth-username”: “”,
“proxy-enabled”: 0,
“proxy-port”: 80,
“proxy-type”: 0,
“rpc-authentication-required”: 1,
“rpc-enabled”: 1,
“rpc-password”: “transmission”,
“rpc-port”: 9091,
“rpc-username”: “transmission”,
“rpc-whitelist”: “*”,
“rpc-whitelist-enabled”: 1,
“upload-limit”: 100,
“upload-limit-enabled”: 0,
“upload-slots-per-torrent”: 14
}

transmission-remote-gui

Transmission Remote GUI is a tool to remotely control Transmission-daemon via its RPC  protocol. You can download native applications for Windows, Linux and Mac OS X. In Linux, to make the file "transgui" executable by doing the following,

$ sudo chmod +x transgui