Half-Life 2's Source Engine is the best commercial engine to mod, if you're looking at any sort of first-person game, in my opinion. It's highly robust, includes full out of the box support of a number of powerful features, is widely compatible with a number of useful tools and plug-ins, and has one of the largest and most supportive communities. As far as programming for it is concerned, its source code is among the most well-documented and cohesive I've seen, and it's also a great way to learn about the higher order functions of CPP such as OOP, polymorphism, and inheritance.
But with Unreal Tournament 3 on it's way, who knows what might happen? I'm sure that one of the reasons that HL2: Episode 2 is being delayed is for a much needed engine update to make it more competitve with UT3's shiny new hotness. But again, who knows?
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