Sometimes, for example, when processing Russian tex-files, it is needed that texify invoke not bibtex but bibtex8 with some options, or not makeindex but some other program to make extra preprocessing before makeindexing. Unfortunately, as far as i know, there are no options in TeXify to specify which program must be run "as bibtex" or "as makeindex". Of course, this can be done by specifying the needed programs in BIBTEX and MAKEINDEX environement variables, but such a way is not very convenient and definitely is not applicable in portable versions of MiKTeX.
So, to my mind, it would be useful to implement MiKTeX 2.8some extra options controlling interaction between texify and bibtex and makeinex. Sorry, if I am ignorant and such a feature already exists