The temperature of the ocean below 1000 m
General Information

One major operational system for the measurement of deep sea temperature, salinity and pressure is the Argo program. Individual Argo floats are distributed in the worlds oceans. Their measurement data are scientifically evaluated and are available for public download. Additionally, several research institutions own gliders. However, I am not sure if they are also used operational for deep sea measurements.

Argo floats

Argo floats are large submerged buoys. They are made for profiling the top 2000 m of the world's oceans. The common depth of an Argo floater is approximately 1000 m. Approximately in 10-day intervals they sink to 2000 m depth and afterwards rise to the sea surface, from where broadcast their position and measurement data. Currently, more than 1000 Argo floats are active in the worlds oceans.

The official Argo homepage is here. Here you find a more detailed description of the function of Argo drifters and here you can download drifter measurements.

Gliders

Gliders are one tool for measuring temperature and salinity on vertical transects (actually not a purely vertical transect). Some gliders can go below 1000 m. The disadvantage of a glider is that it needs considerable horizontal space available straight ahead of his direction of motion. 

A nice explanation and applications are given here and here.

This is the homepage of the global scientific glider community.