From experience on the B4 Passat much is the same as Golf 3 so all the usual Golf issues such as eating ignition coils.
They seem to need top strut mounts regularly, the central locking system can leak and the cv joints arent always the standard Golf ones. Mine seems to have a passion for chewing ABS pumps but its a Teves MkIV which seems to be a very fragile system - brakes are good though without ABS so its not too much of an issue.
As you say the gearbox is a weakness so check that carefully. The other thing that seems to be an achilles heel is the front door window regulators. Apart from the Golf 3 slide issue the mounting screws seems to work loose causing the window regulators to wear prematurely towards the top of the travel. The regulators are handed and not interchangeable with anything Ive been able to find and are damn expensive so make sure there is no play in them.
The ignition switch aslo seems to play up. Check all the electrical equipment works before buying - wipers a/c lights etc. Two or three devices (cant remember which but I think wipers blower fan and headlights is indicative ignition switch is shot. Just changed one a month or two back and didnt enjoy the experience!
Generally seem to be a better car than they look imho. I went from a brand new BA Futura that kept locking its gearbox up to one and I prefer it so ditched the Futura. Best of luck!
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