I personally prefer the executable file... Especially when HFS is always being updated, i am a bit old school and i prefer to download the entire new application than run an update on a program.
Also i like to save HFS options by default to file, i dont like the idea of saving to registry... MAYBE we could have a
single save file (Save Settings) that you could save out the virtual file system, the options and whatever files HFS needs to save to a file, i have noticed the template also stores itself in the same folder as these.
BUT on the upside, it is true that an installer would be good for the people that are a little freaked out by executables... i like them myself, i even run utorrent from an executable

MAYBE the version with the installer could include "approved" HFS templates within its installer... and maybe the user can build their file system, add in a template from the supplied selection or from a file... then once the install is complete they have a fully operational HFS, file system and everything nicely setup !!!