I'm still trying to figure out whether one should use pdftex or latex when compiling .tex source files.
It seems like there are a few advantages to using pdftex over latex. 1) It's faster, 2) Leaves behind fewer junk files (like .dvi and .aux) and lets you go directly to .pdf which is a more modern file format than .ps, 3) Apparently it works better with the hyperref package (hyperlinks inside the .pdf document), 4) The .pdf generated by pdftex is guaranteed to look great whereas you might get an ugly .pdf if you use the command ps2pdf on your .ps output file from latex. The only advantage of latex over pdftex is that there are some packages which are incompatible with pdftex, most notably psfrag.
A short discussion can be found near the bottom of this blog post.