For other, more complete bibliographies of the editions of Aquinas's works, see:

Thomas Aquinas in English | A Bibliography 

Aquinasonline.com/texts/

Jean Pierre Torrell, Saint Thomas Aquinas: The Person and His Work. 3rd ed. Washington, DC: The Catholic University of America Press, 2023.

In General

For academic work, you should always cite the best Latin edition of Aquinas's writings (see above). With that said, it is okay to also cite an existing print translation. You should never cite the online translations or online Latin texts, such as Corpus Thomisticum and Isidore.co/aquinas (see below), however useful these may be in the actual research process. The list of editions and translations below is far from complete. 

With that said, the editions you should cite in academic work are usually prohibitively expensive and, in the case of the Leonine edition, too large to lug around. For the most part, then, you'll have to read Aquinas in some other edition. In general, the best edition to read is the new Aquinas Institute Opera omnia. This series of Aquinas's complete works is still in production, however, so there are gaps in what is actually available. These are well-designed 8 1/2– 11 blue, faux leather volumes with Latin-English facing columns. The editing is not always great, so you have to be wary. But they have large margins for notes and are very readable and reasonably priced (~$50–60 / volume).

Aristotelian Commentaries in English

Aquinas's commentaries on Aristotle's Physics, Nicomachean Ethics, Posterior Analytics, Metaphysics, De anima and On Interpretation were published in English translation (no Latin) in the Dumb Ox series by St. Augustine Press. Unfortunately these have pretty small margins, so they are not great for taking notes. The Posterior Analytics commentary translation is not the best one available, in my opinion, but, for the introductory essay and notes by Richard Berquist, it is worth owning the book. James Weisheipl, OP's translation of the Posterior Analytics (Magi Books, 1970) is better since it leaves a lot of technical Latin terms untranslated. Some of the translations in the Dumb Ox series, such as John Oesterle's In On Interpretation translation and Kenelm Foster's In De anima translation, are also available from other publishers. I'm not sure if the Dumb Ox version replicates the notes. In general, I would opt for buying the Aquinas Institute edition if it is available over the Dumb Ox one since it includes the Latin.

Aquinas's commentary on On Sense and What is Sensed and On Memory and Recollection was published in English translation by The Catholic University of America Press (no Latin).

Other Philosophical Commentaries

Aquinas's commentaries on the Liber de causis (Book of Causes) (trans. Richard Taylor) and on De hebdomadibus (An Exposition of the On the Hebdomads of Boethius) (trans. Schultz and Synan) were published in English translation by The Catholic University of America Press. The Liber de causis translation does not include the original Latin, but the In De hebd. translation includes the Latin from the Leonine edition. Both have great introductory essays and are very well edited and arranged. Aquinas's commentary on Boethius's De trinitate was published by the Pontifical Institute of Mediaeval Studies in two volumes in an English translation by Armand Maurer under the titles: Faith, Reason, and Theology (qq. 1–4) and The Division and Method of the Sciences (qq. 5–6). Maurer is a very skilled translator and these works include detailed notes, but not the original Latin.

Aquinas's commentary on Pseudo-Dionysius's Divine Names was recently translated by Michael Augros (Thomas Aquinas College) and published in a Latin-English facing edition by the Thomas More College Press. 

Commentaries on Scripture

The best place to get Aquinas's commentaries on scripture is the Aquinas Institute, which includes the Latin, Greek, and English of the scriptural passages on which Aquinas comments as well as Latin-English facing columns for Aquinas's commentary itself. With that said, for a study edition with notes of Aquinas's commentary on the Gospel of John (only English), there is a three volume edition by The Catholic University of America Press.

Opuscula

For Aquinas's opuscula, besides the Aquinas Institute version, there is also a translation of Aquinas's On Being and Essence by Armand Maurer. This is a great translation and has detailed notes, but not the original Latin. Joseph Bobik also translated and wrote full commentaries on On Being and Essence (University of Notre Dame Press, 1988) and On the Principles of Nature and On the Mixture of the Elements (University of Notre Dame Press, 1998). Aquinas's treatise On Separate Substances was translated by Francis Lescoe (Saint Joseph College, 1959).

Disputed Questions

Aquinas's On Evil (De malo) was translated by Richard Regan (Oxford, 2003) and by John and Jean Oesterle (Notre Dame, 1995). His On Truth (De veritate) was translated in a three volumes by Robert Mulligan, James McGlynn, Robert Schmidt (Henry Regnery, 1952–1954). This is edition is well-formatted with large margins for notes, but it is very hard to find, and it is not a good translation anyway. Aquinas's Disputed Questions on Virtue were translated by Hause and Murphy (Hackett, 2010) and by Ralph McInerny (St. Augustine's Press, 1999). Aquinas's Quodlibetal Questions were translated by Turner Nevitt and Brian Davies (Oxford, 2019).