Booksmart. http://www.blurb.com/booksmart
Ultramixer, http://www.ultramixer.com
jAlbum, https://jalbum.net/en/
VRL Studio, http://vrl-studio.mihosoft.eu/
Centigrade UI Components, http://www.centigrade.de/en/products/bizlaf-stock-look-and-f...
Synthetica UI Components, http://www.javasoft.de/synthetica/
JGoodies UI Components, http://www.jgoodies.com/products/smart-client/
SQL Developer from Oracle is also quite ok.
The sample applications developed on the "Filthy Rich Clients" book, http://filthyrichclients.org/
You can watch the related JavaONE 2008 session at
http://www.oracle.com/technetwork/java/j1sessn-jsp-155597.ht...
Oh and MATLAB is also a Swing application.
jEdit, IIRC, was often mentioned as a properly written java GUI app, I think it's Swing, but I might be wrong.
EDIT: IDEA code is apparently open https://github.com/JetBrains/intellij-community