Musical examples should be clear, easy to read, and accurate; in other words, think them through carefully before you set them up. Sloppy notation and slip-shod diagrams or tables ruin even the finest research or thesis papers.
Avoid simply xeroxing, cutting and pasting your examples into the text. Effective examples, whether copied by hand, xeroxed from printed scores, or processed electronically, should be reduced (and sometimes edited from their original sources) to fit the proportions of the text and page, then pasted and recopied (or electronically imported) into the text to give a polished, "printed" appearance.
You will find that examples copied in ball point pen reproduce better than those copied in pencil or calligraphic ink.
Notation software solves many of the old problems in this regard, and it is
worth the effort to learn to use programs such as Finale and Sibelius.
Whichever system you use, be consistent and strive for clarity above all.
Remember to cite the sources for your examples in all cases.
No absolute rules for setting up musical examples have been established. Instructive suggestions are found in Helm and Luper, and in Holoman. Some general rules to follow:
Fl. Hn. Timp. Vla.
Nicknames of scenes can be given in quotations.
When two or more texts are sung simultaneously, they appear as:
Nuper rosarum flores/Terribilis est locus iste by Guillaume Du Fay