I am looking to present content across different Document Libraries from different Web applications. Is there a custom Content Query Web part existing?
The CQWP cannot support this.
You can connect to the other web applications using SharePoint designer and talk to SharePoint using web services (or RSS). However, I do am not aware of whether that limits you to a single list or cross-list.
The list of web services is available on MSDN.
Alternatively look at the Lightning Conductor webpart from Lightning tools which permits cross-webapp CQWPs.
I dont know if you found a way to do this by now but:
We have created a webpart we call "global list view" that can list things over the web application scope, to be able to separate the ALM cycles between intranet portal, collaboration portal, quality management portal, BI portal.
With that webpart you can list documents, items and so on between web applications and filter by managed metadata and regular site columns. To be able to do this, we need to bypass the security and let the application pool accounts have access to the diffrent Site collection databases in SQL. It is not recommended performance wise either, but we have not had any issues yet.
It is a complex custom webpart in 2010 and you rly need to weight pros/cons. In SP 2013 you can use the content search web part if you can live with the latency time between indexing.