The path to latexpdf and latexmf get cut when you upgrade to El Capitan. You have to rebuild the link with ln -s in terminal, or you can just add the path to whatever Latex frontend you're compiling from. In SublimeText 3, for example, I just put the following as one of the paths in LatexTools under SublimeText -> Preference -> Package Settings -> Latex Tools -> Settings - User:
/Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin
i.e.:
"osx": {
// Path used when invoking tex & friends; MUST include $PATH
"texpath" : "$PATH:/usr/texbin:/usr/local/bin:/opt/local/bin:/Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin"
// Path to PDF viewer, if needed
// TODO think about it. Also, maybe configure it here!
},