Version 0.2.6 on SVN can now run as a daemon and be controlled by command line or JSON-RPC.
On Linux it needs libgtk2.0-0 installed, but does not need a GUI running. Hopefully gtk can be installed without having a windowing system installed.
The command to start as a daemon is:
bitcoin -daemon [switches...]
Or, to run the UI normally and also be able to control it from command line or JSON-RPC, use the "-server" switch.
bitcoin -server [switches...]
With either switch, it runs an HTTP JSON-RPC server that accepts local socket connections on 127.0.0.1:8332. The port is bound to loopback and can only be accessed from the local machine, but from any account, not just the user it's running under.
To control it from the command line, the interface is a command name without any switches, followed by parameters if any.
bitcoin <command> [params...]
bitcoin setgenerate true
It's a simple JSON-RPC client and prints the JSON result. Look at rpc.cpp for the list of commands.
Web apps or anything automated will normally use JSON-RPC directly, not command line. There are JSON-RPC libraries for all the major languages. In script languages like PHP and Python the syntax is as natural as calling a local function.