Hey Seibtrono's, let's start off by not beating around the bush: Transformers animated series(and to a certain lesser extent, comics) are made to sell merchandise. Luckily for us, it's usually integrated into the story fairly well, and brings us into the Universe it creates rather than out of it. However, there are times when the product placement becomes a little too blatant, and you shake your head at it.
Here's my quick list, and yes your mood may vary:
The begining of the G1 episode "B.O.T." comes to mind. Bruticus is formed, just to be blown apart by the previously unseen Defensor. The rest of the episode isn't much better, with several shout outs to the Protectobots and Defensor in general.
Continuing on with G1, how about Sixshot's apperance in "The Rebirth"? Five up, five down, and never to be seen again(at least in the U.S.).
Let's move to Beast Wars, specifically Season 3. In my opinion, most of the Transmetal 2 "upgrades" were rather pointless. Yeah they were decently integrated into the story, but I really feel like the stories were catered to have the upgrade occur, and they were so spaced out with few status quo episodes in between to really help us see what a difference the upgrade made.
Dinbot 2 would get a pass since he was essential to the final episode, but the entire episode "Proving Grounds" really felt like an excuse for the audiance to see how cool he was, with little else happening in the episode overall.
Tigerhawk I think does get a pass though. According to the TF Wiki Hasbro didn't know if they were going to make his figure so his early demise could be forgiven. As for his introduction episode, it did tie up a loose end from Season 2, have a couple major impacts to the overall story, and did no worse showcasing the character any different than previous intro episodes.
Now let's highlight a couple in Armada. The first, Overload. Yeah, he had no impact in the series overall, but for the record I do enjoy his figure. The second would be Optimus Prime's color change in the final episode. No reason given, no apparent power boost, just an excuse to sell a repaint.