First, thanks for the link at the end of your article :)
Well, there're several aspects of taking photos with built-in cameras in PDA's.
First, the quality of the lens system. The most important thing; the one that can't be fixed from software.
Second, the quality of the JPEG compression algorithm, its parameters. If the built-in software ("Camera" in HTC-manufactured devices) is faulty at this, a third-party app will be of great help.
The built-in "Camera" app (I’ll refer to it as "Camera" from now on) isn't at all bad when compared to some older camera applications shipped with CF/SD-based camera cards. With them, CECam, the most widely known third-party camera app for the PPC, helped a lot (see for example Gerard’s posts at Brighthand on this question; for example,
here ). With “Camera”, the problem isn’t topical any more because “Camera” already has a decent JPEG compression algorithm, which can’t really be made better.