The 2004 Cowboys v Roosters prelim already got a mention, so here's some more:
The 2012 Decider (TM). Qld awarded a try from a clear obstruction, which ultimately sealed the game (and the series) for them.
2014 Game 2: NSW are all set to win the shield back for the first time in 8 years, having just scored from Trent Hodkinson. From the kick-off, with less than 10 to play and the Blues up by 2, Sharon Woods doesn't get out of the way and the ball grazes him. But the officials don't want to look at it again, not when history could be made. Game on, series win Blues.
The 2016 dead-rubber. NSW play like absolute rubbish and Qld are all set to sweep the series, but cleansweeps are bad for the concept of Origin (TM, Ch.9, betting agent) and it's also Paul Gallen's last ever Origin game so strings are pulled all night to keep NSW in the contest. Right when it looks like the game is done, NSW arse their way to a miracle try so Gal gets his final conversion kick, chaired off a winner and Laurie Daley keeps his job for another 12 months (in hindsight, a grave mistake). Even Joey Johns is grumbling after the game at the blatant stitch-up job that favoured his side all night.
The 2019 Decider (no TM, as it was at Accor and not The Home Of Origin (TM Ch.9, QRL). NSW are cruising when Tyson Frizell is penalised for an "escort" penalty, the likes of which happen dozens of times normally with no penalty in a regular game. But Qld need a try to keep the contest alive, so penalty Maroons. Tramp Stamp scores from the ensuing set of 6 as the commentators gush about how amazing it is that this happens time and time again in Origin. Thankfully, justice prevails as the Blues stage their own miracle try in the dying seconds to win the game- and the series. According to JT in the post-match, NSW were "probably the better side" but this is ok because it's JT so it's just #passion, not at all a #whinge like Joey does.
2020 Game 1: With NSW trailing and a minute left, Felise Kaufusi gets to hold down in the tackle and drain the clock for a full 30 seconds unpenalised. Even after this time wastage, NSW appear to have one last shot at glory, but the ref blows full time right as Cleary looks to dive for the line and score. It doesn't matter, so long as millions of Qlders and the betting agencies are happy.
2020 Game 3: Fox is chasing a kick and taken off the ball when he is all set to score and tie up the Decider (TM) late in the game. In any other game it'd be a penalty try, but not this time because...reasons. It ultimately proves the difference as the Worst Qld Team Ever (TM Paul Gallen, QRL, The Courier Mail) wins the game and the series. Thank goodness KWEEEEEEENSLANDUH!!! is an actual thing, not at all influenced by 50/50 decisions going their way in Decider(TM)'s, otherwise Origin as we know it would have died years ago.
I guess Origin really is different...