State Saves
In addition to emulating the native save types, Project64 is also capable of saving the entire state of itself - everything that it needs to know to recreate an exact point in time during the emulation of a particular game.
can be broken down into two types:
slot saves ("Quick Save")
named saves ("Save As..."
A game saved and loaded in this way does not "know" that it has been saved and loaded - it is as if the interruption never happened. This is clearly something quite different to what you can do a real N64. This is called "state saving", the resulting file is a "state save" or "saved state", and will be relatively large compared to a native save file.
State save files will not be compatible with other N64 emulators unless they explicitly support the Project64 state save file format (at the time of writing, several do). It is worth noting that a state save file will also save any errors that may have occurred and be present in the memory of the emulator, and for this reason, state saves are generally less reliable than native saves, especially over a long period of time playing.
To provide you with more flexibility in state saving, a number of "slots" are provided. A "slot" is simply a number, which is associated with a particular keyboard key so that you can select the file with a single button press. The advantage of slots is that you save switch between quickly, the disadvantage is that you might have trouble remembering what you put in each slot! Every game has its own independent set of 11 slots, so don't worry about one game overwriting another.
Save As... just means you can choose a filename and location for your state save file. This is good when you finish a session and want to make a note of where you were in the game.
It is normal for the system to pause for a short while while generating, compressing and writing the save file. The quicker your system, the shorter the pause.