I have been trying both. And even tried SEO Elite.
To answer your question I need to know what do you need software to do. Because some features are better in one of them, others in another.
As for me WebCEO is more comprehensive. But I do not use all of its features all the time. What I use are Ranking check, Link check and partners' links monitoring (sometimes I buy links, but tssss it is a BIG secret

), and HitLens (this is traffic analizator). And sometimes I use built-in FTP-uploader
And of course its reports! With my clients I use Report Viewer and it is the easiest way to provide them with the reports I have seen.
If you need more detailed description just ask

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