I sometimes get asked what I think is SharePoint's weaknesses. No software is perfect and I would rather think about conditions under which you should probably think either about another product or and extension of SharePoint.
The 3 main "problems" I see with the current SharePoint are as follows:
1. Accessibility. This makes me rather sad actually because accessibility is not just about getting disabled people to see your site, but about good structured sites. Sadly the HTML produced by SharePoint is requires massive effort to make accessible to AA or AAA standards.
2. Graphics. Basic modifications are much better in MOSS than under SPS 2003, but still SharePoint is one of the harder tools to make look the way you want. I used to work with Senerna's Collage WCM tool and even now MOSS 2007 publishing features are far inferior.
3. File Plans. SharePoint RM does not support MoReq or TNA FilePlan trees structures. Since almost all existing RM solutions use complex filepans using MOSS as an RM replacement will be very difficult.