The only way to really talk about this is to tally up manuscript finds and literary references. For a baseline, there are a few dozen extant manuscripts attesting to canonical NT texts that can be dated before the 5th century or so, mostly of the Gospels and the Pauline epistles. Some of these manuscripts are very fragmentary, and some have whole texts or multiple texts. Literary attestation started almost immediately, e.g., the synoptic relationships between Mark, Matthew, an Luke, and just increased from there.

On the other hand, the Gospel of Thomas has three fragmentary papyrus finds from Oxyrhynchus, and the more complete Coptic manuscript from Nag Hammadi, all probably from the 4th century. It does have a decent number of mentions in surviving literature, but those are all, as far as I know, in reference to its "heretical" standing. The author will declare that it's popular among some group (Manichaeans, usually) that he doesn't like, and state some heretical thing that's written in it. These references are reasonably accurate--they don't claim things about GTh that are patently untrue now that we have the manuscripts--but it's not always clear that these authors have personally seen the text, or that there was a single version, barring translations. So, it's clear that GTh was well known, at least among a certain type of writer, but less clear how well circulated it was. It's possible that the author of the Gospel of John knew it or the community that produced it, but there's a whole lot of disagreement on that point.

The Gospel of Judas, since you ask, has a single literary attestation in Irenaeus, and a single manuscript. But we can't verify that Irenaeus is definitely referring to the same text as we have from Codex Tchakos, and Tchakos itself was handled so, so badly in the 20th and 21st centuries that we really have no concrete idea about its context. (Don't support the antiquities trade, kids).

The evidence for each text is going to be different. The Shepherd of Hermas seems to have been canonical at least among some groups, and was at any rate widely popular. But some of the texts from Nag Hammadi have no other copies and no external references, and we wouldn't know about them at all without that find. We certainly don't know for sure what roles they played in any particular religious context.

Determining how they were used and by whom is a whole other problem. I've seen estimates that only about one percent of ancient writings have survived to the present day in any form, and that's before we consider that for the most part, the ancient Mediterranean world wasn't a literate society in the way that we think of it. Reading wasn't a necessary part of day-to-day life for most people, and so most interactions with texts like these would have been in group readings or more abstract "It's written in the scriptures" type of oral circulation. If someone didn't write down that they were using the text and what they thought of it, or if their writings weren't preserved, we'll never know. In that sense we owe a lot to the heresiologists, as much as we might not be fans of their attitudes--there are a number of things we might not be aware of if they hadn't bothered to tell us why we should suppress those things. Of course, then interpretation is a problem, because you can't trust them to give an objective picture of what the Nestorians and Manichaeans and Ebionites, etc., were actually doing. To some extent, unless you're working with something extensively attested and/or reasonably preserved, like Valentinianism or Marcion, you can't win for losing.

Geography is also a huge issue--the reason so many amazing finds come out of Egypt and other desert areas is because the arid weather keeps the materials from disintegrating. If someone in Egypt didn't have a copy of something, it almost doesn't matter how popular it was anywhere else, we still might never see it, and the flipside is also true: something could be in use by twenty people, but if they happened to hide it in a dry enough cave or throw it into the right trash heap in Oxyrhynchus, now we have it. So the same criteria that I mentioned at the beginning of this answer can give a very warped perception of the real life of these texts.

It's really a very fascinating field, as difficult as it is to get a handle on. But we have to be really careful about the claims we make about these texts, because after a point there's just no evidence one way or another.