Fonte: http://jabref.sourceforge.net/

JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef runs on the Java VM (version 1.4.2 or greater), and should work equally well on Windows, Linux and Mac OS X.

BibTeX is an application and a bibliography file format written by Oren Patashnik and Leslie Lamport for the LaTeX document preparation system. General information about BibTeX.

Instalando no Linux:
Download o arquivo JabRef-2.1b2.jar

Depois faça:
Logue como root

mude para o diretório onde você baixou o binário:

faça o arquivo executável: # chmod +x j2sdk-1_4_0_03-linux-i586-rpm.bin

rode o executável da instalação: #./j2sdk-1_4_0_03-linux-i586-rpm.bin

Opção 2: Baixe o arquivo j2sdk-1_4_2_12-nb-5_0-linux-ml.bin que já vem com o NetBeans.

# chmod +x j2sdk-1_4_2_12-nb-5_0-linux-ml.bin
# ./j2sdk-1_4_2_12-nb-5_0-linux-ml.bin

Depois de aceitar a licença, um rpm será extraído e colocado no mesmo diretório.
# rpm -Uvh j2sdk-1_4_0_03-linux-i586-rpm

Verifique se o java está em seu PATH: which java

if you get a message saying something like: /usr/bin/which: no java in ....

then you can either make a link to the java executable or add the directory of the executable to the path. The java executable will most likely be in

# /usr/java/j2sdk1.4.1_01/bin/

directory.

So you can make a link to this as follows

# ln -s /usr/java/j2sdk1.4.1_01/bin/java /usr/bin/java

now download the JabRef.jar binary and type in

# java -jar JabRef.jar