Composition markers and layer markers are used to to mark important times or to store comments and other metadata in a composition or layer. In Creative Suite they may go under different names and have different functions than the apps you know best, but markers and their metadata can be transferred between Adobe apps. For more on this, see Sharing markers with After Effects, Encore, and Flash in Adobe Premiere Help.
To learn more on markers in AE, see After Effects Help's Layer markers and composition markers, which explains in depth many aspects of using markers. Of special note is a subsection of that page that lists many scripts and utilities for working with markers.
Basic and useful among them are scripts by Jeff Almasol: Copy Markers and Remove Markers.
Also useful is a new feature in CS4, speech metadata, which imports with layer markers with the transcription as labels. The preference for this feature is off by default (via); the toggle is under Preferences > Media & Disk Cache > Create Layer Markers from Footage XMP Metadata. For additional info and video links, see the earlier post Metadata in After Effects & CS4.