Really, it all has to do with how many lines you have to play around with. But the most important notes are that most of the time need to linger as long as possible are:
the lowest note,
the highest note,
as well as the second-highest note. (This can differ a bit between songs.)
As an example, this part from an MML I made,
See which ones linger?
Here I had 4 lines to play around with, therefore I could be all fancy and let the green note linger too. If I had only 3 tracks I'd let the pink (highest), yellow (second-highest) and the blue (lowest) notes linger. (Also, each rest here is r64).
And I forgot to mention, this example is taken from a piano song, hence why the notes linger so long where-as if you have a lyre you can most of the time just follow Blargel's excellent advice above.
Hope that helps somewhat!