Wing Commander Series:
Supermarine spitfire: tough, fast, reliable, but not as advanced as some other offerings. Still won the war though, at least in its time.

Starfleet Academy:
German experimental "flying-wing" Gotha: Rarely anyone had heard about it, but it was still one of the most advanced aircraft in its time.

Asteroids:
Cardboard box with paper wings: Great fun, but only if you have a greater imagination.

Jumpgate:
F4 Phantom: Well constructed aircraft, with a solid engine, good control, and a well-deserved reputation. Could account for why it's still around today, but only with a small group of dedicated pilots.

Freelancer:
F-22: Long years of development have done this craft well. During development, the design had been changed, scrapped, and rebuilt, all while critics chastised it for being a waste of government money. However, by its release, the wait paid off, resulting in a very well put together piece of machinery. However, due to some rushes to get the thing out in the open, it still retains some flyability bugs, but it's still the best of the best.

EVE online/Earth and Beyond:
Concorde: A great premise in supersonic flight that fell flat. Designed to be the revolution in supersonic passenger travel, passengers soon found out that behind all the hyped-up technology, some serious flaws lurked. Eventually, one of them crashed and burned, and the line was discontinued. The name remains a byword in aviation today.

So, anyone have any more?