One thing that I usually notice about open source games is the lack of a good introduction. With some games this is acceptable — games like Atomix are their own learning curve — but for others it is a serious obstacle to new players. What's the point of writing a sophisticated game, and then giving the player no explanation of what is going on? Some games come with little more than a one-line description, not even making the objective clear. That is why I went to the trouble of writing a proper, albeit ugly, help screen for Kye, and a set of introductory levels.
Undoubtedly the best I have seen, though, is Battle for Wesnoth. Not only does this come with an interactive tutorial, to walk you through the features of the game, but it even has a guided first battle scenario, which guides you through a real game. That's in addition to having a good learning curve in the first real levels. On top of that the game has excellent artwork, and some half-decent sounds too, making it one of the best open source games I have seen.
Doom 3's introduction segment, woven into the game, is the best I have seen recently in commercial games — both setting the scene, and allowing you to get used to the controls. But that's what you pay for in a commercial game, real developer time spent on boring stuff about telling you how to use your PDA; open source games too often fail to put in this effort. But of course Doom 3 takes it much further, using the opening section to providing ominous hints of the coming disaster — and making the later scenes more effective by showing you Mars City before the disaster, so you feel more a part of the crisis when it happens.