Mostly toys, books and videos, I think. But there was also a feature film out a couple years ago too ("Thomas and the Magic Railroad" with Alec Baldwin as Mr Conductor.... parts of it were filmed at Strasburg RR. My girls liked it, but IMHO the series was better.)
There are all kinds of liscensed stuff, shoes, clothes, bed linens, beach towels, alarm clocks, toy boxes... As far as the toys ole Thomas has been offered in lots of sizes. Probably the most popular is the Learning Curve (Brio compatable) wooden toys, followed by the die-cast stuff from Ertl, there's even a "My First Thomas" line of toys for toddlers.
Lionel has sold a couple different electric gauge 1 sets (the bright yellow plastic ties are...interesting), and there is even an n-scale set out. The gauge 1 stuff, even (ab)used, is bringing some pretty good money on ebay. (example: We bought a used "James the Red Engine" set at a train show back in December, we sold off everthing but the lokey and tender...when we added it up the difference, the people on ebay had actually PAID us $47 to keep old James
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One of our little Sara's first consistantly identifiable words was "Du-Du" (choo-choo for those who don't speak baby dutch) Probably due in part to watching some Thomas videos with her old dad (IMHO the earlier stories narrated by Ringo Starr were written a bit better).