A common issue in Microsoft Dynamics CRM is the functionality to use "standard" email functionality, using the buttons in the interface.
Unfortunately this doesn't work for custom entities, only for standard entities. The process checks whether an email address is valid in the standard entities e.g. account, contacts etc.
One of the possible solutions is to make a shadow copy of your record in your custom entity to for example the entity contacts. If requirements need immediately use of email functionality, then you should use web services else you could use workflow. To prevent showing your shadow copies in default view of contacts you should also make new custom view and set this view as default.
These steps would create the basic functionality also you have to consider, what happens when the shadow copy is updated; this could also be realized with .NET or workflow functionality e.g. a scheduled service who synchronize these records.
Have fun extending :-)