This series by Peter David seemed to get a lot of love from DC in the early part of the run, evidenced by the number of special issues produced. After Sins of Youth, the series pretty much was self-contained. There are a couple of sneaky crossovers that are not apparent at first glance.
Girlfrenzy: Young Justice – The Secret
JLA: World Without Grownups 1-2
Young Justice 1-2
Young Justice 1000000
Young Justice 3
Secret Origins 80-Page Giant
Young Justice 4
YJ Secret Files and Origins
Young Justice 5-8
Young Justice 80-Page Giant
Young Justice 9-10
Young Justice: No Man’s Land Special
-YJ #1000000 was published between #2 and 3, hence it’s placement.
-Secret Origins 80-Page Giant and YJ Secret Files and Origins have clear notes within themselves and the issues around them regarding placement.
-Young Justice 80-Page Giant is a little more vague as to whether it could go before or after YJ #8.
-YJ in NML is probably the hardest of the early specials to place, because it doesn’t have many context clues. It came out the same month as #10 (the end of a 2 parter starting in #9), but due to ongoing subplots with Red Tornado, I had concerns about where exactly to place it. However, his appearance in NML is minimal enough that it’s easy to ignore any potential continuity issues, so I leave it in publication order.
-Optional: Red Tornado story from JLA 80-Page Giant #1. His final appearance before mentoring Young Justice, it can go sometime before YJ #1.
Young Justice 11-12
Young Justice 13
Young Justice 14-19
Young Justice: Sins of Youth 1
Young Justice: Sins of Youth Secret Files and Origins #1
Sins of Youth: JLA Jr.
Sins of Youth: Aquaboy and Lagoon Man
Sins of Youth: Batboy and Robin
Sins of Youth: Kid Flash and Impulse
Sins of Youth: Starwoman and the JSA Jr.
Sins of Youth: Superman Jr. and Superboy, Sr.
Sins of Youth: Wonder Girls
Sins of Youth: The Secret and Deadboy
Young Justice: Sins of Youth #2
-Supergirl #36-37 are part of a direct crossover.
-Sins of Youth order comes from the SoY books themselves.
-Optional: Impulse #56 between YJ #15-16
Young Justice 20-34
Young Justice: Our Worlds at War
Young Justice 35-36
Young Justice 37-40
-As far as I can tell, even though YJ #36 ends with “continued in Superboy #91 and Impulse #77″, only Impulse #77 is needed to smooth out YJ plots. Superboy #91 reads more like an issue designed to recap other parts of the crossover for the sake of the ongoing series.
-Some folks like to include Impulse #78 after YJ #37, but there’s maybe two pages that are really important to YJ, and I feel like it’s recapped enough in YJ proper to not need.
Young Justice 41-44
Young Justice 45
Young Justice 46-55
-Impulse #85, Robin #101, and Superboy #99 are part of World Without Young Justice (beginning/ending in YJ #44-45). The first half of Robin #101 could possibly be skipped.
-There’s one story thread at the end of YJ #45 that continues into Impulse #86. Even though there’s not a lot of YJ in that issue, I included it to smooth over the plot. But then #86 continues into #87 and has even less YJ (almost none). Still, including it to smooth over the plot, but I’m drawing the line there.
-Optional: Spyboy/YJ #1-3 is written by PAD and partially drawn by Nauck, but has quite a few mixed reviews. It doesn’t appear to affect the ongoing series at all, so I left it out, but some maps place it between YJ #40-41.
-Optional: Titans/YJ: Graduation Day #1-3 is a mini-series that occurs after YJ #55 that transitions Titans and Young Justice into Outsiders and Teen Titans. I feel like it generates more story threads than it wraps up, so I prefer to keep those issues in my Infinite Crisis collection.
Also, note that Young Justice #9 can be difficult to find for a decent price. Apparently, some character that became a thing on a TV show debuted in that issue, so the internet thinks it can get some extra money for that issue.