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Ronald D. Moore himself admits that the second season episode "Black Market" is a huge Wall Banger, and it has not been referred to since (apart from the death of Fisk).
The ultimate stand-alone episode (third season, natch): "The Woman King." Michael Angeli "Helo" thwarts a racist serial killer doctor who didn't exist before and is never heard from again. Everyone carries a gigantic Bigotry Ball so Helo can be the hero.
So, we had two more doctors in the fleet that weren't apparently utilized? And one was a brain surgeon?
Fridge Brilliance: with 40,000 humans in the fleet, including many from affluent backgrounds, there should be more than one doctor; but they would have their hands full working in the civilian fleet. Presumably, it wasn't until the refugee situation on Galactica that another doctor had to be brought on board full time. This is confirmed when they bring in that brain specialist to treat Anders' head injury.
It does work by Rule of Symbolism, but they didn't try another blood transfusion after the relapse. Real Life cancer therapies often take more than one round; why not this? And they didn't use the fetal cells to synthesize a cancer cure. Doc Cottle will wish he'd thought of that if his years of chain-smoking catch up to him.
The whole New Caprica debacle as a whole. You do not start suicide-bombing against a race who is for all intents and purposes invincible when they, if sufficiently angered, can simply take off and nuke your planet from orbit, that being the only way to be sure. Now, they were using said suicide bombers to kill the people volunteering for the new Cylon police force, hence discouraging people from co-operating with the enemy, but the "nuke your planet from orbit" problem still stands. Maybe it would make a bit more sense if there weren't only 40,000 human beings left - a number that drops rapidly in any case.
The ultimate fate of the Pegasus. A year before what happened on New Caprica, Lee proved he was worthy of command by holding off three Basestars for several minutes until the jump drive was up and working again. This makes his decision to sacrifice the Pegasus, a more-heavily armored Battlestar which could produce brand-spanking-new Mark VII Vipers, ridiculous. Lee knew his father's plan and what would be happening on the surface: get the launch keys to every grounded ship and fighter and take off seconds after you've dusted off the surface. There was no reason to ram the Pegasus into the Basestar; there was no one left on the surface, and the Cylons wouldn't have known where they were jumping to.
When Lee arrives at New Caprica to save Galactica, the best plan he can come up with is to get in front of the guns/missile tubes? How about blowing them away? Why not launch another full missile spread like the one that destroyed a Basestar seconds earlier? Nice job breaking it, Lee.
Battlestar Galactica's Grand Finale is considered the grossest of its Wallbangers by some, and they were building up throughout the third and fourth seasons. They got rid of all that remained of their advanced tech. Those whom the finale bothers do not believe that there is a reasonable In-Universe reason for the Colonials to do that, or at least that the reasons that are given in the episode are valid. The plot is forced by a Temporal Paradox that no one In-Universe is even aware of.
At least they gave the robot Cylons all their tech so they can, you know, form a peaceful Empire.
This quote from one of the moderators at RPGNet should pretty much sum up what was wrong with the Grand Finale.
The worst part? Forget Dark Age. We're talking Stone Age.
Every single human and Cylon in the fleet seemed to have absolutely no problem with abandoning their entire civilization, culture, and lifestyle. Maybe you could get the higher ups to agree with this plan, but you definitely couldn't get thirty-nine thousand people to agree with abandoning every single thing their lives have been built upon to "go native" for no apparent reason.
The only thing—the only thing—that the "idea" had in its favor was that with breaking-down tech, limited manpower, and no industrialization, it was inevitable. But that's like committing suicide for no reason but "we all have to die sometime". They took the worst possible course of action.
"A Measure of Salvation". The Galactica crew get their hands on a biological weapon that could have been used to destroy the Cylon race entirely. When they discuss a plan to use it, Helo argues against it, claiming ethical problems with genocide (even against a race that has made the humans' lives hell for the past few years and are intent on committing genocide against them), but makes an unbelievably idiotic statement defending the Cylons' actions during the New Caprica occupation. Regardless of Helo's objections to this plan, Adama and Roslin decide to go through with it. So Helo destroys the weapon before they can deploy it. And the rest of the crew don't find this out until the worst possible moment, when they've engaged the Cylons in battle and attempt to deploy it. Galactica narrowly escapes, and Adama and Roslin realize it was Helo who did it, but Adama decides to ignore the whole thing. Regardless of the ethics of what they tried to do, the fact remains that Helo committed treason, violated the chain of command, and put Galactica (and, by extension, the entire fleet) in grave danger in doing so. And Adama decides to just let him off scot-free. He's threatened his other officers with execution for stuff like that.
Probably because he realizes that considering genocide was simply just dropping down to the Cylons' level. Though the "not telling Adama the weapon is a dud before he sends the fleet in on a virtual suicide mission" part definitely deserves an airlocking nonetheless.
The worst part is that when you look at the cylons they have no civilians. Every single one is part of their military in some way so it's not like they would be killing a whole punch of children who never did anything, they would just be killing enemy soldiers.
Word Of God is the the repercussions for Helo were meant to be addressed in "The Woman King", but see the top of this page.
Also pretty painful is how all the lines of the argument that Tigh would normally say are randomly assigned to Lee, where they come off as very out of character, due to Tigh being Achilles in His Tent at the time.