This would not affect Eclipse, no, but it does affect locally produced applications that are distributed from an intranet web server with Java Web Start / Java Network Launch Protocol.
Previously, we could just self-sign our app and users could choose to accept the app once and for all and not be bothered so long as the signing cert didn't change. Now, all of our users running Java 1.7.0_40 are given the threatening dialog each and every time they run our internal app, and they can't get rid of it.
We're going to pony up for a code signing cert from a (Java-recognized) certificate authority to make the dialog go away. It's a hassle, but probably still the right thing for Oracle to do at this point.