This is a great topic, and I encourage you to make such a master list. When thinking of these "self-deprecating meta-references", it might be good to bear a couple of things in mind:
First, who is speaking the lines? Although we sometimes tend to ascribe lines to Shakespeare himself, his characters represent a variety of different and sometimes opposing perspectives. As a character who is often more of an observer than a featured participant in the action, Fabian seems like he might represent Shakespeare's perspective, but because we can't possibly know what Shakespeare actually thought, it might be wiser to note the potential similarities than to equate them. As a fairy jester (and the only character in A Midsummer Night's Dream who can inhabit all the worlds of the play: the fairy world, the world of the mortals, and even cross the boundary between the performance itself and its audience), Puck also seems to represent a kind of omniscient or outside perspective. Yet, there are things that he can't see and do as well. In 3.2, Oberon reminds Puck that "we are spirits of another sort", reminding him that the fairies aren't always tied to night (and death) in the ways that Puck often suggests throughout the play. This suggests that for all of Puck's versatility, he doesn't have an ultimately reliable perspective either.
Second, metatheatricality was a popular convention in early modern drama--and not just in the works of Shakespeare. Beaumont's brilliant play The Knight of the Burning Pestle has a metatheatrical framework that emphasises the play's wild satire. Drawing attention to the play as a play was not unusual, and while boasting might bring an unfavourable audience response, gentle self deprecation might tend to urge a more positive one, especially if the author really felt that the play was pretty solid.
Statements like those you've mentioned above may be a little akin to a host or hostess dismissing their masterpiece main dish as 'nothing' to their guests, even though they may have spent great time and effort working on the meal--it is a form of polite, accepted social engagement that may well have been regularly practiced in the early modern age as well.