I was disappointed that I only caught some passenger trains, but that Oakland spot is very photogenic. If I lived there I would definitely get the schedule down and hang out there for freight traffic.
Getting back to the Wine Train, I guess it all depends on your level of interest and your budget. If you're just looking to photograph the train itself, you can show up at their maintenance spot and get some decent photos. Plus, the train moves pretty slowly along its route, which parralels the road, so it's easy to catch and there are plenty of crossings to pull off at, plus the train's stopping point where they change the engine for the ride back.
As far as the cars themselves, you can pretty much walk through and photograph every one regardless of what ride you paid for, although the dome car is technically roped off at the top of the stairs for the people who paid to be there. If it's in your budget to ride in the dome car it is worth it, mainly for the view/ride. The food wasn't bad but you can pretty much get it a la carte in other cars and you're really paying for the view of the dome car. All of the cars are nice inside. You can get pretty good shots out of the train as it travels from many points, and good shots of them switching the engine around when it stops and prepares to return.
I was out there as a special occasion and opted to throw the $ down for the ride, otherwise, I might have chosen to just catch the train on its route and photograph it from the outside.