This tab contains several has been redesigned and expanded in IGB 6.6. This tab contains options addressing the color/appearance of non-track elements in the image, as well as some other miscellaneous options. 
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Coordinates
The options for changing axis appearance are here. You can change the foreground and background colors or customize the format used to present numbers. Changes to the colors take effect after closing the Preferences window.
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Changing Number format to FULL shows the number with no thousands separators and the unit 'kb'. COMMA shows the numbers with commas at every 10^3 (U.S. style) and with no unit designations. This is the default. ABBREV will show the numbers as abbreviated as is reasonable, with unit designations. For example, when zoomed out, numbers appear as 10M, 20M etc. Changes made here to Number Format take effect immediately. 
ORF (Open Reading Frames) Analyzer
These preferences affect colors used to indicate stop codons and the ORFs shown in the Sliced View tab. After setting new color options, uncheck and recheck the Analyze ORFs option in the Sliced View tab to show the new color scheme.
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Residue Colors
IGB highlights each residue in a different color when zoomed in. In this section, you can change color settings for residues. By default, IGB uses cool colors for A and T residues and warmer colors for G and C residues. Other refers to residues that are either 'N', 'X' or '-' (missing) and can be set to a bright color if you are looking for deletions in short read sequences; otherwise you may wish to leave it as the neutral gray. Changes made in this section are immediately applied to the image.
Tip: If you do NOT wish for individual residues to be highlighted, set the colors to white or a light grey. Another great color scheme, if you are looking for CpG islands, is to set A and T to a neutral white or grey, make C a bright red and then G a moderate blue - this makes it easy for the eye to pick out the CG combination when skimming across genomic DNA.
Miscellaneous Options
ORF (Open Reading Frames) Analyzer
These preferences affect colors used to indicate stop codons and the ORFs shown in the Sliced View tab. After setting new color options, uncheck and recheck the Analyze ORFs option in the Sliced View tab to show the new color scheme.
NEW! Edge Match
Miscellaneous Options
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IGB has included an option for the Prototype - View Mode, which will automatically change the default view to a depth graph view as you zoom out past a threshold. Details can be found Prototype - View Mode.
Confirmations
IGB warns you when you are about to exit the program, before you delete a file or files, and before you attempt to load alignments data (BAM files) for very large regions. Each of these warnings has the option Do to not show be shown again. To turn off these warnings or reset your previous choice, check (or uncheck) Ask before exiting, Confirm before delete and/or Confirm before load.
Zoom Stripe Options
The Zoom Stripe is very useful for knowing your genomic location and for seeing the horizontal zoom focus. However, sometimes the Zoom Stripe label (genomic location) can impede your view of data. Unchecking Show Zoom Stripe label will hide this information. You can hide the zoom stripe entirely by unchecking Keep zoom stripe in view. This is useful sometimes when making images for publication or slides.
Reset all preferences to defaults
Click Reset all preferences to defaults to reset all the preferences to the IGB defaults. This is sometimes useful if you need to troubleshoot IGB. Be careful, as this action will reset ALL preferences and will also cause IGB to forget the location you were last viewing. 