There's a menu config file in ~/.fluxbox that allows you to set your preferred browser and terminal. You'll also notice that fluxbox-generate_menu doesn't pick up executables that start with capitalized names (i.e. SciTE) unless you do something like "ln -s /usr/local/bin/SciTE /usr/local/bin/scite" (it doesn't pick up firefox because it gets installed as firefox35, not simply firefox). It's annoying, but that's the only real annoyance I have with fluxbox (otherwise it's my preferred WM on all *nix machines I use).
Also, look into ~/.fluxbox/usermenu. It's exceptional useful, too.
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