Not been reading on here very often recently. I'll try and write this well so someone can Wiki it for all (E D I T spelling as you see fit

).
The basic setup, as fitted to all turbo diesel engines (N/A diesels don't have aux pumps)...
The aux pump, mounted high at the front of the engine bay, is triggered by a temp switch mounted in a coolant hose flange off the head (can be in the front hose by the low oil pressure switch or on the side hose just behind the injector pump, along with the almost identical looking temp senders for the heater plugs and dash gauge!). This switch operates the pump when the engines hot, it handles the full current, there is no relay involved! The switch comes on at around 104°C. VW obviously thought if this wasn't reached very often (winter say) the pump could seize up, therefore to prevent this there is a relay in the little lunch box at the front of the engine bay (its the little relay, the big one being the heater plug controller), it makes the pump run whenever the starter motor is energised, thus you should automaticly excersise your pump every time you start up.
Extras for Syncros...
Presumably because the engine is encased in a lot of extra protection which reduces air flow around the engine, VW felt the need to fit a fan to cool the turbo (all diesel syncros having a turbo). This fan runs off a battery feed (terminal 30) via a relay. Relay and fan are both located behind the left hand tail light cluster. The trigger circuit for the relay is the aux pump circuit so the fan should run whenever the pump circuit above is active.
Common faults -
Pumps can seize - test by hot wiring direct to battery, bridging the switch connection to ground is easiest (and checks wiring).
Switch failure - test with multimeter, or exchange with known good one.
Relays failure, usually through corrosion - If it looks manky, replace it (especially the fan relay as its exposed) this might be the initial cause of a seized pump! To test if the anti seize relay is working, unplug the trigger wire off the starter solenoid and try and start the engine (might be best with an assistant). As the starter motor won't now kick in you should be able to hear/feel the pump running when the key is in 'start' (plug the starter back in now so you don't get an unwelcome job next time you go to start it (after refitting engine lid)).
Switches can get mixed up! - This ones took me months to figure out! The temp switch looks almost identical to the coolant temp senders, and have the same plugs (see below). A multimeter in diode mode should ID a switch or sender in situe. With a hot engine, swapping the temp guage wire between sensors works well too, it should read simular for the dash guage and glowplug senders (which are the same) and eather cold or overheat for the pump switch, as its eather open or closed. If you do connect the pump wire to a temp sender you should find the pump will be running a lot of the time the engine is remotely warm. Most likely to notice this on a syncro as the turbo fan will be on very frequently, you might also notice the fan sometimes not running when the pump is (which shouldn't be possible). A side affect is a low battery if not used for over a month. Reason for this is as the water cools, rather than the switch turning off, the sender just adds more resistance lowering the voltage and slowing the pump, not turning it off! Eventfully the voltage gets too low to trigger the fan relay but the pump will always be slightly live, draining your battery! If you plug the heater plug wire to the pump switch the glow LED will usally preheat for 12sec cold or warm, probably easy to overlook. Don't discount the possibility you don't have the right switch fitted, on mine I had 3 temp senders and no switch, which explains why it couldn't be fixed swapping like for like as I initially tried. Later style plugs are colour coded (see below).
Finally, as with everything, faulty wireing - look for the worn out burned bit, probubly that bit someones bodged in the past.
Parts used...
- Pump, found in most VW turbo engines as well as VR6's
251965561B or 034965561C - ETKA reckons the second one is the van part (which I find odd as the first one is a T3 part number!) I suspect in reality they are interchangeable.
- Relays - Standard 4 pin 40A automotive relay. 141951253B or "53" as far as VW is concerned (they use them all over the place, as do other manufacturers)
- Switches/senders- There are two different styles of switches used.
- Early ones screw into a metal pipe flange with an M10 thread. Terminal is a single spade terminal (earth through flange).
Temp switch for pump = 251919521, colour unknown (other models, LT)
Temp sender for Coolant gauge/heater plugs = 049919501, colour black (other models, many inc cars)
- Later switches are 2 pin 20mm sensors with an 'O' ring seal that clip into a plastic pipe flange. They are connected via a "Junior Timer" plug with a spring clip you need to press to release.
Temp switch for pump = 251919369F, black with yellow (other models, LT, Passat 97-2000 (means available from car dealer!)
Temp sender for gauge/glow plugs = 251919501D, colour black with green (other models, many inc cars)
'O' ring = N 90316802 (dimensions 19.6x3.65 apparently)
Clip = N 90316802 (shouldn't need one but its there if you do)

Later style pump switch (brand new, about a tenner (2008). Note yellow crayon marker. Sadly this isn't visable when its fitted, same story with the part number stamped on it.

Later style temp sender for gauge (used), along with "Junior timer" plug. Note the green crayon is practically invisible through age, needs part number reading to ID, YES that plug IS colour coded!
Junior timer plug colour codes (from memory, resisnably sure its accurate):-
Black, coolant temperature gauge
Red, heater plug relay for temp signal
Brown, Aux pump