"Junk DNA", like "gill slits", seems to now have more of an "historical" ring to them than anything else. Sure, creationists use them as ammunition (we know how they love their dictionaries), and they are misleading, but I don't think they are going anywhere.
So, I think that if the terms are used, we should be sure to use them in the proper context - i.e. with others who will know what you are talking about.
Interesting about transposons and such - some creationists argue that functional pseudogenes is evidence against evolution, while others argue that they are bad news for the concept of post-Fall degenration.
They should probably get their stories straight.