Many model railroaders have a favorite flag (railroad company), so a logo decal would be one option. If he has no favorite, a collage of logos could make a cool pen.
If you want to cast actual model railroad parts, most are too big for pens - but there is T scale, 1:450. Track rails are just 1/8" apart, and a car/engine is only about 1-3/4" long. There's not much in the way of US trains available, but there are some 60' box cars (midway down the page at
Distributor & Dealer for T-Gauge (1:450 scale) the smallest operating model train scale from K.K. Eishindo (Japan)). One of those sliced in half lengthwise would get you two cars to put on a pen barrel. The track might be small enough to be cast as well (you'd probably have to remove a lot of the plastic roadbed - or get the flex track which has no attached roadbed).
If he's into operations, other decal possibilities would be scheduling diagrams or track schematics. If he's got a favorite model company, you could do their logo (such as the Lionel logo presented above).
One more possibility comes to mind: you could use model railroad scenery materials and paint to make a miniature scene wrapped around the pen - much smaller than any actual model railroad, but using the right colors and materials it would be unmistakable, I think. The tracks and trains would just be painted in. (I'm talking about esentially a birds-eye view of a layout that wraps all the way around the pen.) Of course, this would then be cast in clear resin.
Just a few quick thoughts from a model railroader...