The only 3rd party scenario I've ever been able to beat was Tempus Irae (I was never able to beat Evil or Red, and I've never played Rubicon) but I'd still like to see a sub-story page dedicated to them. We have to remember that there really aren't very many games for the Mac, and that Marathon is pretty old, so we owe these dedicated programmers a great debt for keeping the spirit of Marathon alive. (It would have stayed alive regardless, but they helped out A LOT)
As for my favorite game of the trilogy, I' d have to say Marathon 1, which was ironically the last one I played. Even though I already knew the story I was blown away (Both literally and figuratively) by the style, tension and atmosphere. I liked Marathon 2, but felt it was the least original of the Trilogy. I loved Marathon Infinity's plot line, but I agree with [Tycho] that the level design simply wasn't that good. I thought it they were too big and that the mission objectives were too vague. I also liked the M1 textures, especially the gloomy magnificence of the alien ship. The M1 alien ship texture is still my favorite in any FPS.