It breaks down to this..
Most of the games should run fine with the default settings.
For audio you only have two choices, Azimer, which is the audio source from apollo used with jttl's SDL sound output, or PJ RSP, which is the basic audio plugin with LLE.
If a game is not playing (as in loads and freezes, or runs slow) you may be able to tweak the preformance by adjusting the memory settings.
The best way to go about this is to load the game, and turn on the debug display by right clicking on the analog stick and selecting it.
This will display how much memory is free. Start playing your game and keep in mind how much is free.
A example would be...super smash brothers. Ingame while your playing you have say.. 7.5MB free on average.
Quit the game and go back to the romlist and go into the settings.
The default setting should be 4MB video.
For 1964 dyna should be 8mb, and paging 4mb.
For PJ64 dyna should be 16mb, and paging 4mb
Now you will want to adjust your settings dependant upon which emulator you used.
Keep in mind that in order for the menu ingame to display correctly, you need atleast 4mb free. With 7.5 mb free on our example, that would give you 3.5 mb to play with, if you want the menu to show. If you dont give a damn about the menu, then i would suggest only going as low as 2mb free, which would give you 5.5Mb to play with.
The most noticable impact you will see is by increasing the dyna. Only in very few games (like super smash brothers and banjo tooie that comes to mind) need alot of video memory for textures. You'll notice some backgrounds missing in SSB if your video setting is too low.
So, by default, say in 1964 you have 8mb dyna. You have anywhere from 3.5-5.5 MB to play with. My suggestion would be to trial and error and see what does best for you. Try increasing the dyna by 4mb first, and see if that improves your preformance. If that doesnt work, increase it by 2, and increase the paging by 2. If that doesnt improve, drop the paging to 2mb and increase the dyna by 6mb.
Some games, like perfect dark, simply need more memory than a 64mb xbox can provide with the current core. It needs about 16mb dyna and 16mb paging in order to run smooth.
In some cases you can drop the paging to 1mb without a noticable difference. This may increase stuttering, or draw the FPS to nothing when trying to load a level/scene/texture that requires large memory.
If you have anymore questions please ask.