I Reaper it was very easy to save off a combination of instruments and effects as a 'FX Chain' but I'm not finding any equivalent way of doing that in Studio One. What am I missing, or is this just not possible in the current version?

From the manual:

6.5.2 Music Loops
A Music Loop consists of everything required to recreate a musical performance, including the
virtual instrument preset, multichannel FX chain presets for the virtual instrument outputs, the
music-performance file, and an audio loop. Music Loops can be dragged in from the Browser,
just like a MIDI file, but they are much more powerful in that they can re-create the exact setup
used to make the original performance.

And

6.5.1 Audio Loops
Audio Loops are essentially Audio Parts tagged with a tempo and rendered with lossless
compression. To create an Audio Loop, drag any Audio Part to the File Browser. You will then
see the Audio Loop listed, along with a drop-down arrow in the Browser that, when clicked,
reveals the Slices that the Audio Loop contains.

Audio Loops allow fast creation of flexible audio loops from any source. For instance, you
might take part of a drum recording you just made and turn it into a loop by doing the
following:

• Export a stem for the Drum bus for the desired range to a new stereo track.

• Detect transients on the new track and then apply the Slice action, with the Merge
option checked in the Audio Bend panel.

• Drag the Audio Part to Browser to export an Audio Loop you can use in any Song and
can share with other Studio One users.

Why don't you watch Groove3 Studio One tutorials with this offer?:

http://www.groove3.com/str/access-it-all.html

http://www.groove3.com/str/studio-one-training/

there are "fx chains" for insert chains and "music loops" for combinations of instrument presets and fx chains for their output-channels as well as a demo part with an audio preview. (both are explained in the manual, but it might be enough to know that both are created easiest by dragging to the browser, either the insert header or an instrument part)

Well that's kind of a funky round-about way of getting the job done. So much for good workflow but it does work, even with an empty midi clip. I guess I'll create a folder to put track templates in. It's not exactly elegant though.

Ultimately I'd like to be able to save off a folder in the same way, with its composite tracks, that would be cool. But I don't want to save off all the midi clips that would be inside it.

I thought it was alot easier than all that jazz. So you have your insert or send tracks with all your effects on them, grab the title bar of that chain where it says 'insert' or 'send' directly from the mixer and drag it over to the browser window. That should let you save the whole thing as a preset. The only thing is it wont save instruments, only everything on the insert/send path, but at least you get all your effects in one preset

If you look in the browser under effects there should be a folder named 'Fx chains', thats where all the built in chains live and you can store your own there

Yeah but that is only for effects, not including the instrument. To save with instrument you need to create the midi file from what I can tell. It works just is not very elegant, it is more of a workaround using one feature not intended to be used in this way.

http://www.mutools.com/mux-product.html

This does what I was looking for, I'm still getting used to it but it is pretty cool I am wondering what the eventual price will be.