Confusion in choosing between JavaGit, JGit and EGit

You can use JGit as standalone library, but, as mentioned in the JGit Homepage:

JGit can be found within:
* EGit, Eclipse team provider for Git

In that sense, JGit is connected to Eclipse in that EGit uses JGit features to develop the Eclipse Git plugin.
Considering all Eclipse projects are now versioned in Git repos (instead of previously CVS repos), I would consider JGit for your Java project, as it seems that:

• JavaGit isn't updated for quite some time (2008)
• Eclipse is committed to offer a good support for Git through EGit, which should ensure by extension the development of JGit (used by EGit).

Thorbjørn Ravn Andersen comments:

Even though you say that Egit uses JGit, it is not quite clear in the above that EGit is an Eclipse plugin for git giving git support in the same way that CVS is already supported in Eclipse

The migration of Eclipse projects from CVS to Git is in progress, and has been reported here (by Chris Aniszczyk).

I’ve monitored conversations concerning the migration of project code from CVS to Git in the dev-lists of several projects.
Most developers, it seems, understand the value proposition of migrating, despite their concerns that with migration comes a whole lot of new learnin’ as they figure out how to say productive in the new environment.

Inevitably, discussion about the team provider for Git being developed by the EGit project becomes an prominent part of the conversation. “Is EGit ready for primetime?” is often the question that bounced around

The official bug illustrated Eclipse commitment to provide "adequate tooling support" for all Eclipse projects now on Git repo is the bug 293192.

In order to deprecate old VCS in favour of git (bug 270854), adequate tooling should be available. This bug is created to track that.
[...] I opened/linked relevant EGit bugs in order to have a better visibility/tracking of what's missing.

So Egit is the only project referenced in that bug to provide said adequate tooling support for the new (D)VCS chosen for all Eclipse projects.

(bug 270854 is about Deprecate old VCS tools, which includes essentially CVS.)

Just in (March 17th, 2001): The State of Git at Eclipse – Early 2011 (Chris Aniszczyk):

I’m happy that things have come quite a long way since last year based on Eclipse Marketplace stats and the community contributions the projects have received.

So what’s next? In terms of tooling, we’re getting closer to our 1.0 release (which is planned for the Indigo release).
The git tooling at Eclipse is much better these days, if you need help or have questions, please start with the most excellent EGit User Guide.

If you’re an eclipse.org project, please consider starting the process to move your project repository to Git. There are a lot of eclipse.org projects already on Git.
It would be nice to see the all of the eclipse.org projects have plans to move to Git by the Indigo release.

As one of the authors of JGit and EGit, sorry for the confusion.

JGit is an EDL (new-style BSD) licensed, lightweight, pure Java library implementing the Git version control system. It can be used in a standalone fashion and is embedded in applications such as Gerrit, Eclipse, Netbeans and IntelliJ. EGit embeds JGit to use it to work with Git repositories and expose Git constructs from within Eclipse. At the moment, JGit doesn't support the git-bundle command but you're welcome to contribute support, it shouldn't be that hard, please see our contributor guide.