<p>We've got a fairly large amount of code that just made the jump to Java 5. We've been using generics in those components targeted at being released in the Java 5 version, but the remaining code is, of course, full of raw types. I've set the compiler to generate an error for raw types and started manually clearing them, but at the present rate it'll take a <em>very</em> long time to go through with it (there are about <em>2500</em> errors). And that's with Eclipse's helpful Infer Generic Type quick fix, which always gets rid of the errors, but often generates code that needs further work.</p>

<p>Is there any better way to dealing with this? Are there any automated tools better than Eclipse? Any way to apply the refactoring to <em>all</em> occurences instead of doing them one-by-one? Or do you just ignore the warnings?</p>

I would suggest ignoring the warnings.  Otherwise, you'll be putting a lot of time into updating the legacy code without making any improvements to its functionality.
Update:
Great comment from
Luke
that I thought should get more visibility:
"Generics are a way to catch run time bugs at compile time. Unless this legacy code has bugs in it that you think are related to casting I would leave it alone (if it ain't broke, don't fix it)"