When I did my big readthrough of all of Batman's "Year One" stories (and related tales), there was perhaps one very notable omission: Batman: Year 3 by Marv Wolfman, Pat Broderick, and John Beatty, which was originally published in issues #436-39 of Batman vol. 1 in 1989. This is because Batman: Year 3, unlike Batman: Year One, Batman: Year Two, or indeed spin-offs like Batgirl: Year One and Two-Face and Scarecrow: Year One, has never been collected.
When you read it, though, it's easy to see why. Year One and Year Two were both interruptions to the ongoing narrative of Batman. Even though they originally appeared in issues #404-07 of Batman vol. 1 and issues #575-78 of Detective Comics vol. 1, respectively, they had nothing to do with what preceded or followed them-- they were sort of miniseries within an ongoing series. Year 3 is different: it was published between A Death in the Family and A Lonely Place of Dying, and has a frame story set during that time, with Batman dealing with the emotional fallout of the death of Jason Todd (Robin II) at the hands of the Joker.
"Frame story" is actually kind of misleading, as I would estimate that probably more of the story is set in the "present" than the "past." Year Three is when Dick Grayson's parents died, and he became Robin; the present-day storyline partially deals with the fact that Dick's parents' killer, Michael Zucco, is about to be released from prison. The flashbacks we see are primarily to provide context for this: the death of the Graysons, the hearing where Bruce adopted Dick, Dick's introduction to the Batcave, Dick's training and debut as Robin, and so on. (Much of this would later be re-depicted in Dark Victory and Robin: Year One.)
This means the bulk of the story focuses on Zucco's imminent release, and a gang war occurring in Gotham at the same time, which Batman handles with much more brutality than is typical. Part of the purpose of flashbacks is to show how parterning with Robin caused Bruce to soften from the Frank Milleresque way he was depicted in Year One-- and how now that a Robin is dead, his old brutality is reemerging. Wolfman is very good with the characters of both Bruce and Dick, and between this and A Lonely Place of Dying, I would definitely read more Batman stories by him.
But Wolfman's success with this is probably also the reason this story hasn't been collected. Batman: Year 3 is a good depiction of how Batman started to fall apart following the death of Jason Todd, but despite its title, it's not a very good standalone adventure in the early years of Batman: it's no Year One, that's for sure, but it's not even a Year Two. It ought to be collected, but not on its own. Better would be along with Wolfman's A Lonely Place of Dying, as it sets up Batman's need to always have a Robin, and Tim Drake (who becomes Robin in Lonely Place) even puts in a cameo at the circus during the flashback to the death of the Graysons.
Batman: Year 3 originally appeared in issues #436-39 of Batman vol. 1 (Early Aug.-Late Sept. 1989). The story was written by Marv Wolfman, pencilled by Pat Broderick, inked by John Beatty (#436-38) and Michael Bair (#439), colored by Adrienne Roy, lettered by John Costanza, and edited by Denny O'Neil.