Collections

You can serialize collections, but there are some caveats.

Which collections

Currently, only some collections are supported.

Those would be: Lists, Arrays, and Dictionaries. Support for more of them will be added at some point in the not-too-distant future. Adding support for custom-made collections is also planned, by having an interface that your custom collection should implement. But, alas, not yet.

Collections of references and the RefWrapper class

A variable of type List<GameObject> (or List<Component>, or any other UnityEngine.Object) is a collection of references. This would technically work with the current serialization system, but it would create some issues with the Pending References System. And by "issues", I mean the pending references would be entirely ignored. I felt this half-working, half-not behaviour would create a lot of confusion, so I made the call to make collections of UnityEngine.Object not a thing.

Rejoice!

But, good news! You can still serialize collections of references. You just need to add a RefWrapper around the reference itself. List<RefWrapper<UnityEngine.Object>> serializes just fine, and maintains your references, including those that are pending at the time of loading.

//these will not work
[SaveThis] List<GameObject> a;
[SaveThis] Transform[] b;
[SaveThis] Dictionary<int, Collider> c;

//but whese will!
[SaveThis] List<RefWrapper<GameObject> > a;
[SaveThis] RefWrapper<Transform>[] b;
[SaveThis] Dictionary<int, RefWrapper<Collider> > c;

Why do collections of naked references not work?

As I said, it's because of how the Pending References system works. Essentially, the system stores a MemberInfo variable that holds information about the Field or Property that wanted to get a reference. You can think of this as a reference-to-the-reference (not really in the sense of C-style pointers-to-pointers, this is just some Reflection data, not actual memory addresses).

Sadly, as far as I know there is no way to get a similar thing for elements of a collection, because any specific element in the collection is not a member of the collection's class. Therefore, there is no way to recover the variable that wanted to get a reference when the referenced object does become available.

Collections of collections (...of collections)

Nesting collections works just fine. I'm just pointing that out because it sounds like the kind of thing that would cause problems. But no. It's fine.