I have an old 4×4, despite its age it is very popular in Australia, Africa etc and Nissan has retained manufacturing rights to most of the parts for it. That means the parts are rare and expensive. My gearbox has had it (long story) and I'm having it rebuilt. At the moment its in bits at the garage and the mechanic has a long list of parts it needs (ie, its going to be expensive, will find out how much tomorrow).

In the meantime I posted on the Nissan 4×4 Owners forum and I've been offered this:

In my garage I have a 5 speed manual Y60 4.2D gearbox that has done 5,000 miles… yes 5,000 miles.

It was from an almost new 1993 Patrol. The owner of said vehicle complained that there was a problem with it, his vehicle was road tested by many Nissan technicians who all said the gear box was fine. The owner was adamant that he wanted it replaced under warranty.

Eventually Nissan offered to replace the box as a gesture of goodwill and, due to its size and weight, it was never returned to Japan.

I was keeping the box for my Y60 but alas, I think it now needs more than a gearbox

Question: He says "Open to offers" – but what on earth should I offer? There are none on the market for me to compare costs with.

How much is a new one? I'd then quarter it and see if he will take that plus fit it for you – at a complete guess – I'd offer £250 for the box (I have no idea how much these things cost either) plus £100 to have him fit it (assuming it's a bona fide garage).

2nd hand box with questionable lifespan – I'd not be looking past 250 quid on any car. If It was freshly rebuilt I'd probably go to 500 unless it was something really special. I recently got a gearbox (still in production and sells for £2500) for a crate of beer.

As above, work on the assumption it's knackered – it's unlikely the main dealer would have replaced a perfect gearbox just to shut a moaner up, more likely they would have removed the old one, cleaned it really well (or painted it) then shoved it back in telling customer it was replaced.
If you have your's rebuilt with new parts you know it will be good for a long while, i'd start at 25% of what the rebuild will cost you but not go over a couple of hundred, unless he's happy to fit it and let you fully test it before parting with any cash.

In answer to the original title, I normally offer something embarrassingly lower than what I'd expect to get it for, sellers usually then come back with what they think is fair.

my only frame of reference is MG gearboxes which are 4 speed.

£300-£450 depening on their year, oddly non syncromesh ones cost more to re-build than syncromesh ones?

Is he offering any sort of guarantee at all that it will work? Seems to me that hes covered himself and its a punt in essence. Price your offer accordingly. Personally I'd say £200 with the caveat 'more if it actually works' as an agreement.