There's lots of options, but they come with differencing costs, effectiveness, reliability, compatibility, and ability to handle lots of traffic. It's a spectrum all the way from fully automated operation (like you see in some overseas metros), down to 'be ready to stop if you see something' (goods yards).

Auckland has ETCS Level 1, which provides cab signaling and speed limit info, and stops trains before they can SPAD or over speed. But the equipment is only fitted to the EMUs, not locos. The train needs to know all its braking characteristics and the track slopes etc., or you have lots of false activations.

Wellington has conventional signaling, with tripcocks at critical signals. These raise a lever on the trackside when the signal is at danger, which trips a valve applying the brakes if a train passes it. Again, only on EMUs. A complete redo of the signaling interlocking, along with the installation of ETCS L1 (or similar?) and wrong line running is expected in Wellington in the next decade

Main trunk lines are mostly conventionally signaled, with limited cab signaling in the central NIMT (installed with the 80s electrification). Branch lines are often Track Warrant Control, meaning you radio the signaller to get permission for each section of line.