I tend to agree with others here- especially Soraz and Smaci.
One thing I'll add, though. If you do feel that the OS L&F is too constraining, and you have good grounds for going beyond it, I'd strive to follow the priciple of "Pacing and leading" (which I'm borrowing here from an NLP context).
The idea is that you still want to capitalise as much as possible on your intended audidences familiarity with the host OS (there will be rare exceptions to this, as Smaci has already covered). So you use as much as possible of the "standard" controls and behaviours (this is the "pacing") - but extend it where necessary in ways that still "fit in" as much as possible (leading).
You've already mentioned some good examples of this principle at work - Visual Studio, even Office to some extend (Office is "special" as new UI styles that cut their teeth here often find their way back into future OS versions - or de-facto standards).
I'm bringing this up to contrast the type of apps that just "do it their way" - usually because they've been ported from another platform, or have been written to be cross-platform in GUI as well as core. Java apps often fall into this category, but they're not the only ones. It's not as bad as it used to be, but even today most pro audio apps have mongrel UIs, showing their lineage as they have been ported from one platform to another through the years. While there might be good business reasons for these examples, it remains that their UIs tend to suck and going this route should be avoided if in any way possible!
The overriding principle is still to follow the path of least surprise, and take account of your user's familiarity with the OS, and ratio of their time using your app to others on the OS.