But that is because of what I said above...rarity = price increase.
There are only two "competing" Operating Systems for desktop use really: OSX and Windows so why are we comparing Amigas to Apple?
The reason why classic Amigas sell for more it's because of the nostalgia factor. When Commodore was big it had millions of Amiga 4000, 1200, 500 etc... users. People who buy them nowadays are people who know what they are and actively search for them.
Who is going to look for an A1XE or even a SAM? Only the die-hard user who knows what it is.
Also the older the hardware the more appealing it becomes.
Surely you didn't buy a SAM+OS4 as a short term investment did you?
People only know about PC (Windows) and Apple, that is it. The general consumer that is.
And of the two (thanks to its clever marketing/hype/advertising/design and I'll chuck in the OS as well) the iMacs retain more value but that is not to say it's down to the incredible hardware...you can get 5K displays for PCs, I even saw AmigaOS 4 running on a 4K monitor, it looked beautiful...