List Appearances Of Trains In Games

[Artisan]

Let's see here...
Magnet Train - Pokemon G/S/C
TMS Train - Pokemon X/Y
Barrel Train - Mario Kart Double Dash
Spirit Tracks Train - Legend of Zelda Spirit Tracks
Excess Express - Paper Mario The Thousand Year Door
Derailed Express - Wario Land 1 (I'm pretty sure)
Green Train - Mother 3

Any others?

 

[TAG]

Lots of others. If you just mean in Nintendo video games though, the first one that immediately comes to mind is the train in Animal Crossing (the GC version and New Leaf) An iconic way to ride into your new town!

 

[Artisan]

More Trains
Outskirt Stand - Pokemon Colosseum/XD:GoD
Subway Train - Pokemon Colosseum (The Under)

 

[D4rkDragon]

If we need to post appearances of trains in Nintendo games, then, one game comes to my mind:
The Densha de Go! series (From GameBoy to N64, and even the DS!)

 

[Reece]

The train summoning in Bravely Default, Promethean Fire, does that count?

 

[Artisan]

The train summoning in Bravely Default, Promethean Fire, does that count?

I guess that should count.
There's also a train in Kalimari Desert (MK64 & MK7).