The problem with Memory management in the Opcode cachers isn't limited to IIS. Their incompatability is related to FastCGI in general, not IIS in particular. The issue is they allocate memory for every PHP process, not PHP as a whole. The problem is exacerbated by IIS because it's FastCGI implementation spawns no children.
However, the workaround on Apache and Lighttpd that makes APC, Eaccelerator "work" with FastCGI and I put work in quotes because it's still a hack IMO is to reduce the number of PHP processes to 1 or 2 then create a ton of children.
The problem is, this causes one bad child to bring down all of the other children, thus reducing alot of the benefits of FastCGI in the first place which is process isolation.
I just wanted to be clear that this issue should be addressed as an issue with the Opcode cachers as a whole on all platforms. IIS just makes their problem more obvious.
-Stephen