Principal English Translation: 

good, a good thing, fine, well, handsome, pretty, beautiful, well (see Lockhart, Carochi, and Molina)

Orthographic Variants: 
cuali, quali, qualli
Alonso de Molina: 

qualli. cosa buena.
Alonso de Molina, Vocabulario en lengua castellana y mexicana y mexicana y castellana, 1571, part 2, Nahuatl to Spanish, f. 84v. col. 2. Thanks to Joe Campbell for providing the transcription.

Frances Karttunen: 

CUAL–LI.In the modern Nahuatl of Morelos and Tlaxcala the Spanish phrase 'está bien' has been translated as CUALLI CAH, and this has been lexicalized so that the stress may fall on –LI.

Horacio Carochi / English: 

qualli = a good thing; something good, fine, well
Horacio Carochi, S.J., Grammar of the Mexican language with an explanation of its adverbs (1645), translated and edited with commentary by James Lockhart, UCLA Latin American Studies Volume 89 (Stanford: Stanford University Press, UCLA Latin American Center Publications, 2001), 510.

Lockhart’s Nahuatl as Written: 

ca (ye) qualli, very well, fine, okay.
James Lockhart, Nahuatl as Written: Lessons in Older Written Nahuatl, with Copious Examples and Texts (Stanford: Stanford University Press and UCLA Latin American Studies, 2001), 230.

Attestations from sources in English: 

q(ua)ltin yecti(n) = the good ones, the pure ones (linked expression -- cualli = something good; yectli = something good, pure, clean) (Sahagún, sixteenth century)
Susanne Klaus, Uprooted Christianity: The Preaching of the Christian Doctrine in Mexico, Based on Franciscan Sermons of the 16th Century Written in Nahuatl (Bonn: Bonner Amerikanistische Studien e. V. c/o Seminar für Völkerkunde, Universität Bonn, 1999), 243.

yn ixquich, yn qualli yectli, yn tecuiltonolli in tetlamachti = all that is good, delights, and enriches
Andrés Sáenz de la Peña, Manual de los Santo Sacramentos, 1643, f. 33v.; translation by Mark Z. Christensen, "Nahua and Maya Catholicisms: Ecclesiastical Texts and Local Religion in Colonial Central Mexico and Yucatan," Ph.D. Dissertation, Pennsylvania State University, 2010, Appendix E, 12.

ynic amo nelli. qualli limosna yn quichihua yn (8) quipia = so that the alms they make and have are false and bad
Fray Alonso de Molina, Nahua Confraternities in Early Colonial Mexico: The 1552 Nahuatl Ordinances of fray Alonso de Molina, OFM, ed. and trans., Barry D. Sell (Berkeley: Academy of American Franciscan History, 2002), 90–91.

ompa hualtemoz yn iqualtica yn iyectica yn ichipahuanca yn itocã sp sancto = there will descend his goodness, his propriety, his purity, which is called ‘Holy Spirit’ (late sixteenth century, Central Mexico)
Louise M. Burkhart, Before Guadalupe: The Virgin Mary in Early Colonial Nahuatl Literature, Institute for Mesoamerican Studies Monograph 13 (Albany: University at Albany, 2001), 46.

amocualli, amo qualli = bad, a bad thing
cualtitica = is good
ca cualli = very well then
ye cualli = fine, okay
Robert Haskett and Stephanie Wood's notes from Nahuatl sessions with James Lockhart and subsequent research.

Attestations from sources in Spanish: 

Zan ihuiyan, zan icemel ximonemiti, ca ye qualli, ca ye yectli = Sólo con tranquilidad, sólo con tiento vive porque ello es bueno, porque ello es recto
Huehuehtlahtolli. Testimonios de la antigua palabra, ed. Librado Silva Galeana y un estudio introductorio por Miguel León-Portilla (México: Secretaría de Educación Pública, Fondo de Cultura Económica, 1991), 54–55.

qualli = bueno
Pedro de Arenas, Vocabvlario Manval de las Lenvgas Castellana, y Mexicana (Mexico: Henrico Martínez, 1611), 1.

Cuix ticahuaz in amoquali? cuix timonemilizcuepaz = [H]as de dexar lo malo, [h]as de mudar de vida.
Antonio Vázquez Gastelu, Arte de lengua mexicana (Puebla de los Angeles, México: Imprenta Nueva de Diego Fernández de León, 1689), 38v.