A scheme is presented for realizing a quantum phase gate with three-level atoms, solid-state qubits-often called artificial atoms, or ions that share a quantum data bus such as a single mode field in cavity QED system or a collective vibrational state of trapped ions. In this scheme, the conditional phase shift is tunable and controllable via the total effective interaction time. Furthermore, we show that the method can be used for effective preparation of graph-state entanglement, which are important resources for quantum computation, quantum error correction, studies of multiparticle entanglement, fundamental tests of non-locality and decoherence.