I need to think about this more, but you might want to start by looking at
Civilization III, which is considered by many to be the king of strategy games. It's a
4X game, so I'm not sure you'll be into it in the same way as the games you mentioned (I'm not that familiar with them). It's turn-based though, and very rewarding.
Civilization IV is a bit more advanced (in graphics and gameplay), but you might want to consider that as well.
It's true, though, turn-based games (and adventure games, as well) have fallen to the wayside in favour of real-time strategy, 3D shooters, and MMORPGs, etc. I've always enjoyed turn-based. I like to take the time to think. Thinking is fun.
EDIT: btw, I was a huge fan of scrolling space shooters too (including the ones you mentioned). I'm going to look into this. I think there are indie developers of this genre now. I'd love to find a modern game in this genre. The graphics should be real pretty by now.
EDIT2: Here's a start:
:: STARSCAPE :: Voyage into the warp!. Downloading the demo right now. [Update: not bad, but not great]
EDIT3: Apparently this is what has become of "top-down" space shooters:
GameSpot Video: Aces of the Galaxy Official Trailer 1