In testing my answer to this question, I initially wrote the file
%& eplain
% code to answer question here
\bye
and compiled with pdftex e. Much to my surprise, the penultimate line of output was
Output written on e.dvi (1 page, 352 bytes).
If I change the first line to \input eplain or add the command line argument -output-format=pdf, then I get a pdf.
This same behavior can be observed by by starting a LaTeX file with %& latex and compiling with either pdflatex or pdftex so it's unrelated to eplain.

\inputsimply loads the relevant .tex file, whereas first-line parsing switches engine alias. Remember that almost all of the *tex execuatables are aliases for pdfTeX with the appropriate format. So the first line you are using effectively switch the command line toeplain. – Joseph Wright♦ Oct 15 '10 at 7:23.fmtfiles for latex and pdflatex though. It doesn't really seem necessary to have them since one can choose the output format independently of the format file. – TH. Oct 15 '10 at 12:43