In the 'Sequence Diagram' preferences you can specify various global settings. The diagram-specific settings ('Save Image with Diagram as' and 'Show Icons') are stored in the current workspace. The other settings are stored in the configuration area of the Eclipse installation and are therefore the same for all workspaces used by that installation.
When enabled, the option 'Save Image with Diagram as ...' saves an image whenever a diagram is saved. The type of the image can be selected (GIF, PNG or JPEG), the file name is exactly the same as the diagram except of course for the extension. If you save your diagrams with the source code, this should make it easy to integrate images into the javadoc.
The 'Show Icons' option determines if objects should show an icon next to their name and get a light yellow background.
The group 'Ignored for 'Add Called Operations'' contains settings that are evaluated when you select 'Add Called Operations' from context menu of a message. Each setting stands for a syntactical construct that will be ignored when checked.
The 'Ignored Signature Patterns' specify signature patterns that should be ignored when call sequences are reverse engineered. A signature pattern is a Java regular expression as described for the JDK class java.util.regex.Pattern. When you add a Java stack trace, Java stack frames or Called Operations, each operation's signature is matched against all patterns. If there is any match, the operation is not added to the call sequence. By default, the list contains common signature patterns that most people would not be interested in for their sequence diagrams.
There is also a context menu on messages that allows you to add the pattern of that message.
In Eclipse's Colors and Fonts preference page you can change all fonts that are used in diagrams, as well as the colors of diagram nodes and executions in sequence diagrams.