When i come up with architectural ideas around projektmanagement i SharePoint, I very often use the CQWP to aggregate results from Content Types in lists, placed in a lot of sites. So when I had to come up with a sensible structure for a projectmanagementsystem in SharePoint Online, I turned to my trusted Content Query Webpart.
The CQWP has a lot of limitations. You need to semi-hack the webpart to get custom lists shown and you need to know a little about XSLT.
Another limitation of the webpart is that you can only use it to look through 1000 lists. If you have your own SharePoint Server, you can set this throttling, but on SharePoint Online.. Not so much.
This means that if you have 200 sites, with 5 custom lists and one of those lists contains the ContentType your looking for, you’ve just reached the limit. Add one more site, and the CQWP blanks out and shows you nothing. So it’s not the 1000 lists you come up with, but the number of lists it needs to search through.
According to Microsoft this limit is set to prevent performance problems on the server farm. It seems that this limitation is inherited from SharePoint 2007. (http://support.microsoft.com/kb/935502)
So beware of the CQWP on SharePoint Online. It has some big limits. Design your solutions around them.
Here is some more info for those who needs big M’s word for it. http://technet.microsoft.com/en-us/library/cc263061.aspx.