I wish I had an electivire every time suicune reared it's ugly head...
Anyway, I disagree with almost everything everyone is saying.
Azelf? Please, definitely NOT outclassed by aero. Best case for Aero is 6-5 with rocks. Best case for Azelf is 5-5 with rocks. One of those is way better. Not to mention that you could tailor the set to deal with Machamp, Metagross, Breloom etc. Also, Azelf had multiple, multiple lead sets... Screens were excellent, it could do weather, u-turn, what's not to like?
Aerodactyl: maybe. But anyone using an aerodactyl lead knew that they were going to go 6-5 with sr up and their opponents lacking. They weighed this and thought it was worth it. You can disagree, but if a person makes an informed choice that this is worth it for their team, who's to say otherwise?
Gyarados: The hardest part of stall to deal with. Also, sometimes your 100% counter in celebi or vaporeon or whatever would get messed up by a random bounce set. Your counters and checks had to be at high health or else your entire team might be dead.
Swampert: Maybe. But it did it's job of setting up sr, checking loads of random stuff, and roaring stuff away really, really well. Better than other bulky grounds because it doesn't just die to special sweepers, better than other bulky waters because it was immune to sandstream, resisted stealth rock, was immune to electric. And if stuff is running hp grass just for it, then you know it's good.
Flygon: Really good run-away-threat check, scouter, could oftentimes polish off a weakened team with earthquake or outrage sweeps. I can see people not liking it because it was poor against stall and invited opponents to take advantage of obvious u-turning (sometimes), but still, it was the best scout in the game and held together a lot of my teams.
Blissey: One of the main reasons we have a physical metagame? Does NOT just die to random physical attacks? One of the best status spreaders in the game? Can set up sr, pass wish, aromatherapy? I mean, don't put it in some hyperoffence team, but it's excellent in the right team, and a staple of stall...
Weavile, Electivire, Smeargle, Dusknoir, Ninjask: Overrated? No one thought they were good so how were they overrated? If anything they were probably underrated because people just dismiss them as threats...
My vote would be for Roserade. Hard to switch-in, and relatively helpless once sleep clause is activated (though that does mean one mon is out, so that's saying something). It does absorb and set up toxic spikes, but it's offensive presence was quite low despite that 125 special attack. Depending on hidden power, either heatran or salamence/skarm/shaymin was getting infinite free switch-ins... It provides good utility, but is hard to switch in, and is a liability after it does its job.