For a client I had to implement spring based startup module. The module's context xml file simply defines annotation-config and component-scan element and doesn't define any bean. When I add 50-th bean into the module, I reliazed I can't manage dependencies without painting them anymore.
The fast search had lead to 3 nice tools: SpringSource Tool Suite, BeanDoc and Maia EAP. Each one of them may analyze dependencies and may paint them. But no one of them may deal with annotations.