Thanks for your generosity. I'm in for Sword of the Samurai.
Recommending something is difficult since the games you mentioned are quite different and they were all good in their own way. Since everyone has different likes and dislikes I'd rather shortly comment on each of them instead of pointing at one game.
Silent Service 1+2: They were great for their time but these games are more military simulators than actual games. If you are into war simulations (in this specific case submarine warfare) and don't mind reading thick manuals to know how to operate the sub and are fine with 'game play elements' like stalking a tanker for half an hour before you get into the perfect position for releasing your torpedoes at the tanker and getting away before its convoy takes you down then these are the games for you. If you consider such game play a bit too boring you might want to look elsewhere.
Pirates! Gold Plus: Swashbuckling at its finest. This is a classic that hardly needs talking about. Amass a fortune by working for one nation to plunder its enemies, besiege cities, rob (or possibly take over) ships, fence with the enemy captains, find and free captured family members or try to plunder the treasure fleet. You might also think about trading, getting land grants and romancing or even marrying a governor's daughter. So many things to do, so little time until your aging body forces you to retire. This is a truly remarkable game that everyone should have played.
Sword of the Samurai: I have to admit I have not even heard of this game before it came to GOG. But from what I have heard it is somewhat similar to Pirates, with the obvious difference that you play a Japanese warlord in the warring states era who is not only looking for personal riches but also the unification of Japan. That's why I'd also like to try it.
Wing Commander 1+2: If frantic space combat is your thing than these games are definitely for you. This is the mother of all computer space operas. While there were other space combat games before that (like Elite for example) the Wing Commander series was the first to tie up the space battles in a storyline and presented it with almost cinematic direction, even including stuff like a funeral scene when you bite the dust. The space battles can become a bit repetitive over time though. Still, the story and presentation more than make up for that. These are also one of the milestones of computer gaming that everyone should have played, at least in my opinion.
Covert Action: This is also a game I have never heard of before it came to GOG and since I don't know enough to comment on it, I'd rather not say anything. Perhaps someone else can share his thoughts on that game.
Colonization and Alpha Centauri: Both games are strongly related in my opinion. Both are spin offs from the Civilization series. Both are undoubtedly great games. However, I could never really get into those two.
The problem with Colonization is that it only covers the era of America's Colonization. That might be great for an American who feels a strong connection to this era for historical reasons but for a European like me that doesn't do anything. So I'd always prefer Civilization over Colonization because it gave me a whole world to conquer with many more diverse enemies and a far longer timeline to develop my Civilization and its technology.
Alpha Centauri on the other hand is Civilization in space. Sounds great in theory. And even though it is a great game in my opinion it stumbles over its intention to be SciFi. In Civilization you don't need to be a genius to remember what technologies like Pottery, a Granary, the Wheel or Literacy do and what they unlock soon or further down the line. Applying a little bit of common sense is often enough. But WTF is "Matter Editation" or "Quantum Power" and what do you need the "Superstring Theory" for? If you want to play Alpha Centauri successfully you would need to memorize the whole tech tree to know which is the prerequisite for what and what these things actually do or unlock. Some people liked that but I preferred to go back to the far more logical and familiar Civilization.
Should you give these two games a try? Definitely, if you loved Civilization and can't get enough of similar games. Just be aware that you might enjoy the original Civilization series more if you are not into the American conquest era or prefer technologies you understand to SciFi mumbo-jumbo.
I hope that with these short overviews you are able to pick the game you would enjoy most yourself.
