Apart from Deus Ex, Freespace and some other stuff already mentioned, I think the best computer game plots I've seen are in Mission Critical and Case of the Rose Tattoo. They're adventure games from the mid 90s era and need SB16 support, but run fine in Dosbox or Virtual PC. They're among the newer 2D games, so they don't look too bad by today's standards either.
Originally posted by: dighn
Originally posted by: MajorMullet
Indigo Prophecy kept me interested most of the way through
It's too bad that adventure games such as that don't get too much attention. some of them have great story lines and presentation. I suppose the weaker game play turns off most gamers.
They actually can potentially have interesting gameplay, in the sense that they make you think about what the essential properties of various objects are and how they can be used to solve puzzles. It can be quite satisfying to solve the puzzles by thinking through them like this. I've only played a handful of games that really manage to get this right though. Many are either like interactive novels that lead you through everything or, at the other extreme, have obscure puzzles that just require lots of trial and error and for which the solutions don't make much sense.
Among the two games I mentioned earlier, MC is on the easy side but still has some interesting puzzles (and a cool RTS minigame), while the latter is basically the interactive novel type of game.