All features that you would like to offer the user access to through the all-alternates functionality of the Glyphs palette in InDesign and Illustrator. That means, whenever the user clicks and holds on one of the characters in the palette, which alternate glyphs should he or she see in the pop-up. Often, this will be all the GSUB features of your font, but sometimes you may omit some of the features, especially things like "ccmp" if they're only used to decompose your glyphs before additional processing. Sometimes "calt" would also be omitted, depending on the design. Perhaps "liga" and "dlig" should be omitted as well.

In short: include all your one-to-one glyph replacement features there. As far as the other features are considered, make a decision.