Charly Mottet was the last clean general classification contender.
Arguably, Miguel Indurain was clean until 1993, but the performance jump between 1992 and 1993 just isn't human. Either he was already doping and stepped it up, or that's when he started doping. And I love San Miguel enough to give him his own Friendica page @Miguel Indurain (fan)
Between then and the bio-passport, everybody who won anything major blood doped.
Pretty much anybody who follows cycling (on the grounds that most cycling fans are cyclists first, and fans of the professional sport second) has known since 1999 Armstrong doped, but that's not the important part of this. The important part is the corruption heading all the way up to the top of the UCI. He should have had his title's stripped, but as with Riis, those years should list no winner.
Nobody else had early warning of drug tests. They weren't allowed to go for a shower before giving samples. They didn't make "donations" to the UCI following news breaking of positive drugs tests. Twice. They didn't have Pat McQuaid lying for them in public statements. The worst bit is, we don't even know which the lies are - we just know Pat McQuaid isn't consistent with his own statements.
It's unfortunate that things ended like they did - we've got nothing to celebrate until the UCI is either disbanded or entirely replaced...but on the other hand, Armstrong deserves everything he gets. Look at what he did to Lemonde (made the abuse he suffered as a child public, and got his sponsorship deals cancelled), Simeoni (spat on - literally - for talking about drugs), Bassons (harassed out of the sport for being clean), and so on.
Routes are much shorter than they used to be, and all have much better roads (dirt tracks and cobbles used to be normal, now riders protest about them). The Tour de France has fewer mountains than it used to, and less Time Trialling. The Vuelta has more mountain top finishes than ever, but fewer mountains in total, whereas the Giro d'Italia tends to be as hard as it ever was (except this year, which was deliberately "easy"). Of course, because it's shorter, it's also faster...and you can't just compare speeds, because a lot of it is flat, and can be accounted for by drafting.
The closest you'll get to comparing eras is to compare power outputs on the climbs, and it's best to do that for one day races (like classique des alpes - in the mountains, drafting isn't too important) where fatigue isn't a factor, weather reports are available to adjust for wind speed, and the route barely changes.
The clearest way to see why I think "everybody dopes" is to race at a high level (high being top end junior in my case, or amateur-who-gets-invited-to-pro-am-events in other cases). Almost everybody does it. They talk about drugs like we talk about Friendica; it's the one thing everybody has in common.