I'll try to be quick about this, since I've had enough people ask me how to use this goddamn thing and I want to see what other things people can come up with.
Download the program here (link at the very top). Make sure Java is fully up to date, I've heard problems with older Java players not running it.
There are two basic windows in JPM: the Transform window, and the Morph window. Transform is where you create templates for each of your faces, which I'll explain next. The Morph window is where these faces and templates are combined to make the composites.
Before you load up any faces for your templates, I recommend rotating and cropping the faces in an image editor of your choosing (GIMP is a perfect free program for just such a task). Also make sure you save your photos as .png, the Transform window doesn't seem to allow anything other than .pngs even though the morph window can take other filetypes.
Once that's done, go to File -> Load Image in the Transform window and your face will show up. If for some reason your faces are too large or too small to fit properly, just go to the Zoom tab and resize accordingly (I've heard that this may not work for some, but I've had no problems with it. If it does fail, go to Edit -> Resize image and template and resize the file from there).
Now is the arduous task of placing each of your delineation points. I outline my process in this post, you can follow along if you want or you can create your own as you see fit. Just make sure each template is constructed in the exact same order, otherwise you get distortions in the final product; blob face and whatnot.
Once the template is done, head to File -> Save Template and name this template the same as the image file it was derived from. Also make sure that you end the filename with .tem. The program's so unintuitive that if you don't save it in a filetype it recognizes, it won't create any file at all. Be sure you check File -> Auto Load Templates in case you want to go back and fix something later.
You'll also notice that if you have a template already on the screen and you load another image, the pre-existing points don't go away. To get around this I create a blank template files and name them for each new face, so that when Auto Load Templates is checked it automatically loads a new template. This way you can also do Auto Save Templates to save more time.
When all of your desired faces have fully completed templates (and they're all in the same folder/directory), head on over to the Morph window and go to Average -> Make Average List. Save it to the same folder with all your pictures and templates. Name it whatever you want, but make sure you save it with a .txt extension or, like before, nothing will be saved. You'll then see a sequence of pop-up windows: for the first one, select .tem; the second and third choose .png; the fourth will ask you about subfolders, which can be useful in larger projects, but for our purposes we'll say no.
Your finished average list will look something like this. This protocol basically tells the program what pictures go with which templates. You can manually add, remove, or change around files here, but right now we'll leave it alone.
To create your average composite, go to Average -> Average Images. Two pop-ups will ask you for your desired width and height for the resulting image. I personally like to go with 500x600.
Hit submit, and if you've done everything right, voila! It will load up each face in sequence on the left panel, reshape it, and successively add it onto the right side. To better view the composite at this stage, you can go to View -> Display Off to turn off the delineation points. To save your image, go to File -> Save Right Image as whatever file you want; again, make sure to manually add your filetype extension here.
At this point I like to bring the composites into GIMP and touch them up (Brightness/Contrast, color balance, sharpness, etc), or you can just serve it raw. It's up to you.
A couple more advanced tips for ye:
The program has a couple different algorithms for how it generates its composites that I like to mess with. Shape Normalization changes the way in which each delineation point is averaged between each other. I don't know anything about the specifics for sure, but I assume it creates mean averages of each coordinate set based on symmetry or how many outliers there are, etc. I generally find that Full (Procrustes) will yield a better result, but it's always worth a check between that and None. I've never cared for Two and Three Point algorithms, but you can mess with them at your leisure.
Lastly for now are Warping Options. This seems to do with the way in which each individual image is manipulated, although I'm not sure on how the math works. Thin Plane Spline seems to warp each face more evenly, so the final composites generally comes out looking smoother overall. Multiscale generally gives the eyes greater clarity, while Thin Plane Spline makes the mouth more even. Whichever one turns out better results in entirely dependent on the composite at the moment, so mess with both and see which one turns out better.