IKVM and Licensing
Just a quick update on this after noticing the question, for anyone browsing by.
IKVM seem to have updated to use the OpenJDK and not the GNU Classpath, infact IKVM.net have removed the comment from their license page.
There are multiple issues here as ikvm is currently being transitioned away from the GNU classpath system to Sun's OpenJDK. Both are licensed as GPL+Exceptions to state explicitly that applications which merely use the OpenJDK libraries will not be considered derived works.
Generally speaking, applications which rely upon components with defined specs such as this do not fall under the GPL anyway. For example, linking against public POSIX APIs does not trigger GPL reliance in a Linux application, despite the kernel being GPL. A similar principal will usually (the details can be tricky) apply to replacing Sun's Java with a FOSS/GPL implementation.