ifs stands for Image File System. The name is a bit misleading, since although there is a filesystem component to it (the /proc/boot filesystem), it really is much more image than filesystem.
A qfs (Qnx File System), is exactly what most people expect when talking about a filesystem; that is, it is an on disk structure that organizes data into files (and nothing else).
That depends on the application. If you have (lets say) a hard real-time app that consists of a set of fixed processes that do not require any persistant storage, then an ifs alone is probably all you need (i.e. you don’t need a filesystem at all).
If you require persistant storage of any significant quantity then you’ll probably want a filesystem of some sort. QNX supports several different filesystems. The .qfs extension is purely a convention, and usually refers to a “QNX4” filesystem.
One simple way to make a qfs is to copy a partition from an existing device (e.g. “cp /dev/hd1t79 /tmp/foo.qfs”).