(Please note that I don't have specific data on the usages for each of these Pokemon during generations, simply the current tier status of each generation, past some anecdotes through Gen 6. Finding consistent info on tier shifts during a generation seems to be an issue, so I'd appreciate corrections whenever needed!)
Gen 1: Gengar. Starmie was UU for a short period of time in Gen 6, so it's out of the picture. Gengar had a small gap in Gen 3 where it was literally impossible for you to obtain one, after RS but before FRLG, but I wouldn't consider this to be the same as being less-used.
Gen 2: Skarmory and Tyranitar. Scizor is close, but was consistently BL until Gen 4.
Gen 3: As far as I know, None. Jirachi was UU for a short while in Gen 6, and Breloom was BL in Gen 3.
Gen 4: Heatran, Gliscor, and Rotom-Wash. There was a short time where both Hippowdon and Magnezone were UU in Gen 6, but were otherwise OU. Rotom-Wash is kind of a weird one, as Rotom itself was UU in Gen 4; However, all of the Rotom formes were OU immediately following their release in Platinum, so under the same rules as Gengar before I'll allow it.
Gen 5: Ferrothorn and Landorus-Therian. Kyurem-Black was in Ubers for a very short while in Gen 5, before being suspect tested and proved that it was balanced in OU, where it's stuck around ever since. Also, while it doesn't show it now, Excadrill was Ubers for the entirety of Gen 5's popular run, and was only lowered down during Gen 6.
Gen 6: This one's obviously a bit more shaky, for the same reasons as other mid-generation changes, and the megas, in particular, constantly shifted between tiers for a very long time. I do know that Talonflame has consistently stayed up, as has Volcanion (albeit only since its relatively recent release). As for megas, Mega-Tyranitar, Mega-Scizor, Mega-Garchomp, Mega-Latios and Mega-Latias have all stayed in OU, due to their non-mega variants being OU.
Sources:
http://www.smogon.com/articles/tier-shifts - Hippowdon + Jirachi
http://www.smogon.com/tiers/ou/usage - Starmie + Jirachi
https://twitter.com/smogonu/status/464980991384510465 - A very roundabout way to show it, but Magnezone was temporarily in UU
https://twitter.com/smogonu/status/639202026988138496 - Same, but with BW Excadrill
http://www.smogon.com/dex/xy/formats/ou/ - Any mentions of being BL can be confirmed by switching through the generations here
