I'm using eclipse to work on a project with portions written in Java, C, Perl, and bash. Which version of eclipse should I get for this? I'm currently using 3.5-CDT+perl-plugin and would really like better Java handling with out loosing the C. What plugin should i add for java?
Once you start adding plugins, the Eclipse that you start with doesn't matter. They just happen to provide commonly used sets of plugins prebundled - it's the same core Eclipse under the hood. Whenever I've worked with Eclipse, I've always started with Eclipse Classic and added the plugins that I want to use.
As far as multilanguage projects, I can't address that. I've never used Eclipse (or any other IDE) for multilanguage projects. I've used NetBeans with projects of different languages, but each project was of a particular language.
For perl, try using the Epic plugin. Update site: http://www.epic-ide.org/updates
The nice thing about eclipse is that whatever "version" you pick, you can add the updates from other versions (usually) without too many problems. Pick the version you use the most features of, then go back and add additional plugins as desired.
The best Eclipse is the one that installs the cleanest on your current OS setup. Most of the Eclipse issues I've had have had less to do with the language (the exception being PHP) and more to do with my underlying OS. That said, I haven't even had those issues in a couple of years.