Updated January 2013: The latest version of advanced module manager includes support for flexicontent, so there is no more need for this hack.
Advanced Module Manager is a fantastic Joomla extension which allows complete control over where Joomla modules are displayed. The major drawback I found with it is that it doesn't fully support FLEXIcontent.
FLEXIcontent is, for me, a must have extension, which massively increases the control over how articles are displayed and how they interact with each other. I use it for all news, article and magazine websites that I build, the latest example being RusArtNet, where it allows easy displaying of images and linking between related articles.
Luckily a FLEXIcontent user named Rehne produced a hack for Advanced Module Manager supporting allocation of modules based on the FLEXIcontent category:
I've updated this hack to work with the current latest version of Advanced Module Manager (v1.16.5), which you can download here EDIT: link removed. I'll proably update this hack as and when I need the latest version of Advanced Module Manager.