All the Subarus with the 2.5 popped head gaskets until they updated the gaskets or something. Anyhow, I believe the fix was for the '99 year. So '99+ should be good. My sister had an '02 Forester S, 5 speed. She absolutely loved it, however, she rolled it early one morning avoiding a deer. She was fine, and it held up exceptionally well. She now has an '05 92x Aero (Saab version of the WRX wagon), although it's an automatic this time around. Pretty good cars I think, although I really dislike how they drive. I'm thinking you could find an Outback or regular Legacy wagon within your price range, and there is a surprising number of them with manual transmissions. Most of them have heated seats, mirrors, wipers, etc. They seem very durable and have more space than the Forester.
I don't think you'll ever find a Jetta TDI wagon with 3 pedals, for under $5k, so I'd cross that one off your list. I was searching for one a while back. The cheap ones have a billion miles on them. :lol: They're also VWs, so plan for repairs. I like 'em, but you have to be realistic.
I like the Focus idea. Otherwise I'd suggest an Accord, although I don't know if the standard trans was available in the wagons.