I am far from expert, but I thought I would toss off a few, and see if you can't improve on them.
1) Brough.. this was the motorcycle Lawrence of Arabia died on. They cost as much as what a typical Brit earned in a year. Most of them were custom, or semi-custom. They were assembled twice, they were only painted after everything was known to be working properly. George Brough personally tested every one, and rode the SS100 to a 100 mph. That was crazy fast a century ago. And I do mean crazy, people died all the time back then doing stunts like that.
2) The best of the post WW2 Brit bikes, mostly Triumph and Norton. Sure, they had a lot of flaws. But the experience of riding one of the good ones was exquisite.
3) The Honda 750. The first 4 cylinder Honda looked like NASA and a Formula 1 company worked together to build the ultimate bike. No single thing on it was new. But no other bike had put all those things together on one bike, not even close. The Honda engineers must have sweat bullets getting the exhaust pipes perfect. I never again heard an exhaust note as gorgeous as that. Sales guys used to put a cup of coffee on the bike and turn it on. It wouldn't spill a drop, smooth was something new to Americans at the time.
4) I don't know when BMW bikes became great. It took them a while to nail the design down. But they got there eventually, and became perhaps the best bike to keep a couple decades, ride across the continent, whatever.
5) Honda Goldwing, same deal, really. They were rough around the edges to begin with, but slowly evolved into something remarkable. And they keep getting better.
6) Those little Honda motorcycles, scooters, really, that the Beach Boys sang about. I think Honda has sold as many of those as maybe every other motorcycle put together. About a 100 million, yes, million.
Omissions: I don't like Harleys, when I was young they used to break down all the time. They deserve a spot, I admit that, but it won't be me adding them to the list. I also don't like most sportbikes, they are toys. A couple prob deserve a slot. I thought about adding the ST1100, but I'll leave that category to people that like them, and know about them. I couldn't make up my mind about the Black Shadow. It's famous for being fast, but I think there are other postwar bikes that were easier to live with.
So, have at it..