[SpiralOcean]

Part of the issue is most people don't want to put their sensitive information out into the public.

Here is how I deal with some of the issues you brought up:

2) How does anyone using OmniFocus deal with not being able to put single actions on hold? - The lack of this feature just blows my mind whenever I try to use my workflow on a daily basis. There simply are single actions in my projects I want to put on hold, but there just seems to be no way to do so...!

Placing a future start date on an action and setting your context filter to active and Availability Filter to Available is how I hold the item. It then disappears from view until the start date has arrived.

3) Waiting for stuff to be done by others. - I just want to be able to mark single actions with a tag that says "waiting". That way I could just include that tag in a perspective filter (like in Things) and see all my 'waiting for"s without altering their context or place within my folder structure.

I have a waiting for context.
If I am waiting for something to be done by others, I put a future start date on the action. If you filter by available in the contexts, then you won't see the action until that start date.

You can easily put a start date by tabbing to the start date column, then type:
tod for today
tom for tomorrow
mon, tue, wed, thu, fri, sat for any dat of the week
+1m, +2w, +1y, for adding time to today's date.

Every day I go through my waiting for context. Any contexts that are showing up I will do one of the following:
complete
change the start date if still waiting
contact the person if I need to contact them.
send an email reminder and change the waiting for start date until I hear back.

I go through any actions in my waiting for context that are showing up, until there are no actions left in my waiting for context. At which point the context will disappear from the view.

Hope some of this helps.