http://aescripts.com/layer-groups/

Finally, create Photoshop style groups directly in the timeline. Comprehensive functionality to mimic how Photoshop handles groups. One of the most requested features in After Effects. Now with Group Mattes, Isolate layers and Baking of Groups into pre-comps.
Zorro-The Layer Tagger
http://aescripts.com/zorro-the-layer-tagger/

Zorro lets you group layers in after effects by adding tags to layers. Similar to the way you would tag photos in Flickr, you can tag layers in your comps and then select or isolate those layers in groups by using the tags.
Layer Storage
http://aescripts.com/layer-storage/

Custom groups dramatically changing the way you work in After Effects.
Labels
http://aescripts.com/labels/

Take full control over Label Colors - set label colors and select label groups with a single button click. Works both for composition and project panel items.
Isolate
http://aescripts.com/isolate/


Focus on the layers you want. Simple - isolate layers you are working on.