There is nothing that prevents you from designing newer missiles to put into these ICBM bases to make them at least decent when you have some better technology. I usually design some MIRV missiles with size 6-8 missiles as an example.
Later on I upgrade the bases to newer designs or just scrap them when I think they served long enough.
First of all, I don't play conventional starts, but I *love* the ideas put forth by Marc and Jorgen. Particularly for role-playing value, that's awesome.
And as for Mr.Bananza's original question... I'd have to say my early missiles and especially anti-missiles. When you realize that your anti-missiles can't catch enemy anti-ship missiles... well, that's a crappy day.
Past that, I'd agree with Erik. If I have a ship with old launchers, armor, or guns, it matters. But when they have old engines... that really makes them feel antiquated and makes me struggle to fit them into fleet doctrine. And those refits are so expensive.