So I'm a little nervous about purchasing this component and I'm trying to get a really good feel for what I'm going to get myself in to. I think the benefits will be worth it though.

3 Questions:
1. If a component is not in the list of compatible components, does that mean it cannot be used at all, or just not synced from Master to Slave site?

The site I'm hoping to take to JMS uses Joom Donation.

2. If a component uses domain-based licensing, how exactly does that work? Would the Master site need to have a purchased license as well as the Slave sites? An example of this is DT Register or CBSubs.

3. When a new version of a component becomes available, is it required to install the component on the Master and then each Slave site? I'm a little confused about that process.

Thanks in advance, for you time.

1) Compatibility and listed in the JMS Tools is two different things.
Before we created the JMS Tools, the procedure to install an extension was to go in the back-end of a slave site and re-install the extension.
This procedure is still present and can be used when an extension is not present in the list of extension.

Compatibility is something else when you have an extension that does not work, in general it does not work also when you re-install it from a slave site.
In this case, you can send us this extension in the attachement of an email and we will review it and will try to see if there is or not a solution for that.
When an extension is encrypted using IonCube or other encryption system, we can not do anything. This is the same for the one that are using Flash.

2) This is specific to each extension and the way they manage the license themselve.
In general, you have to purchase as many license as you have domaains. This generally does not change the way that the license is processed.

3) See user's chapter 8 that give the full detail.
In very summary, this depends on the type of update or upgrade.
An update that just fix bug and does not impact the DB layout, can only be installed once on the master.
If the extension perform an upgrade and modify the DB layout, add new tables, change existing table, .... in this case you have to re-install the extension in each slave site to let the extension applying the DB layout modification.
Concerning Joomla itself, the bug fixes only concern the PHP code and can be applied only once.

Great response, and I think a lot of that makes sense for my needs.

I've been digging around like crazy to find out if there are issues with the components that my site(s) is(are) using.

One other question: if a new version of an extension comes available and requires the site to be taken offline to update it, such as Community Builder, can the master be disabled and take down all of the slave sites, or does every slave site have to be independently disabled?

Also, I've noticed a few posts about people making changes or "hacks" to extensions and wondering how JMS handled these types of changes... I would still be able to use (Joomla) template overrides through the templates/templatename/html/com_/overridefile structure on a slave site if it needed it, correct?

The On/Off line is a parameter that you select in the Global Configuration.
As you have as many Global Configuration as you have website, you need effectivelly go in the back-end of each website to Enable/Disable the off line.

Concerning the extension that are doing hack in the source code, as long as the does not touch the peace of code that we modifying in the sources, this is not a problem.
JMS Multisites apply the patches on the existing source to benefit of the existing bug fixes and in this case of hack performed by other extension.
When the extension are hacking the same files as JMS Multisites does, you probably need to re-appyly the JMS Multisites patches.