What semiconductor materials are used in the 2N3904?
This particular part uses silicon as the semiconductor. 
If in doubt, go to a manufactures website and query the material breakdown of a component. This information is required 

http://www.onsemi.com/PowerSolutions/product.do?id=2N3904#tab=tabSpecifications

which links to: 

http://www.onsemi.com/PowerSolutions/MaterialComposition.do?searchParts=2N3904

$$
\begin{array}{c|} 
 &amp; \text{Substance}  \\ \hline
\text{Die} &amp; Silicon\\ \hline
\text{Lead Frame} &amp; Silver, Copper\\ \hline
\text{Mold} &amp; Brominated\ epoxy\ resin, Phenolic\ Resin, Antimony Trioxide, fused\ Silica \\ \hline
\text{Plating} &amp; Lead, Tin\\ \hline
\text{Wire Bond} &amp; Gold\\ \hline
\text{Conflict Minerals} &amp; Gold, Tin\\ \hline
\end{array}
$$