MongoDB is fast, but only when your working set or index can fit into RAM. So if my server has 16G of RAM, does that mean the sizes of all my collections need to be less tha
The working set is basically the stuff you are using most (frequently). If you use index A for collection B to search for a subset of documents then you could consider that your working set. As long as the most commonly used parts of those structures can fit in memory then things will be exceedingly fast. As parts no longer fit in your working set, like many of the documents then that can slow down. Generally things will become much slower if your indexes exceed your memory.
Yes, you can have lots of data, where most of it is "archived" and rarely used without affecting the performance of our application or impacting your working set (which doesn't include that archived data).