I used the IBM JDK and JRE for two reasons. This is the one that manages all IBM products (Websphere, Rational, etc.), and connecting to the mainframe is much better.
Also, I used a non-Sun JVM in Ubuntu at home, but now I started using Sun (or Oracle now, I think).
Personally (and this is just an opinion), I would prefer to use Sun for battery life. For things like Websphere, it's best to use the one that comes as part of the product.
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