Adobe Photoshop
Layer Groups (a collection of Layers inside a folder in the Layers Panel) in Photoshop are a great way to organize your Layers — but many times you will need to merge a Layer Group to work on its component Layers as a merged, single Layer as if it were a flattened document. It’s easily done with a keyboard shortcut.
Read more “Merge a PS Layer Group to a New Layer”
Adobe InDesign
InDesign Secrets shared this excellent InDesign script that converts your layered InDesign file to a layered Photoshop file.
Read more “How to export InDesign layers as a layered PSD file”
Adobe Photoshop
Cristen Gillespie has a great article over at CreativePro that will help you understand and use Adobe Photoshop’s Isolate Layers feature. Isolate Layers lets you work on objects without having to search through dozens of layers, locking or hiding everything that might get in your way.
Adobe Photoshop
Layrs Control is a nifty little extension offers you quick ways to perform tedious tasks on layers in Adobe Photoshop. Pay with a Tweetware.
Adobe Photoshop
For the love of God, PLEASE NAME YOUR LAYERS. There’s nothing worse than opening a Photoshop file with 50 layers that are named Layer 1, Layer 2, Layer 1 copy, Layer 4 copy, Layer 4 copy 2 (you get the idea). It makes it extremely difficult to work with later on; especially if that Photoshop file was created by someone else.
Name your layers in a short but descriptive manner. And don’t be afraid to group things into Layer folders. Photoshop even has a Note tool you can use (found under the Eyedropper tool). You’ll have a much easier time editing it later, and anyone else that has to work with the file will thank you.
Adobe InDesign
If you have several layers in your InDesign document, and wish to work with no visual distraction on only one layer, you can turn all the others off quickly by holding down the Option key and clicking the eye icon of the layer you wish to keep visible in the Layers panel. I’ve used this same tip in Photoshop for quite a while, and finally realized it worked in InDesign as well. If you make use of layers, it’s quite handy!
Adobe Photoshop
When you’re using Curves, Color Balance, Levels, Hue & Saturation, and other color correcting filters on your Adobe Photoshop image, it’s always best to use an Adjustment Layer (the icon at the bottom of the Layers panel shown at right). Doing so allows you to make further adjustments to your image later on using the Adjustments panel, leaving the original image intact. It also gives you an easy way to adjust only the gray values in your image, thus preventing color shifting.
First create an adjustment layer using the color adjustment of your choice. In the example above, I’ve chosen Color Balance. Next use the Blending Mode drop down menu at the top of the Layers panel to set the layer blending mode to Luminosity.
Now when you tweak the settings in your Adjustments panel, Photoshop will limit the changes to only the gray values in your image. As you can see in the image above, leaving the Blending Mode of the Adjustment Layer set to Normal introduces a lot of color shifting in the image. By changing it to Luminosity, Photoshop prevents it from taking place.
Adobe Photoshop
Those are some hefty numbers for a Photoshop document. Bert Monroy has made his previous 15,000 layer Photoshop file that took 11 months to create pale in comparison.
Bert’s latest digital painting, titled Times Square, is a 300×60 inch, 6.5 GB flattened Photoshop file features Adobe Photoshop founders John and Thomas Knoll standing in the main foreground, surrounded by digital imaging experts such as Russell Brown and Jeff Schewe.
The Photoshop file on the site can be zoomed using Photoshop’s Zoomify tool, which allows you a close-up view of all the details in the image, and they are amazing!
Adobe InDesign
Adobe has built-in a handy shortcut into InDesign that allows you to hide all the layers in your document except the one you wish to focus on.When you have a lot of layers in your document and want to work on the objects on one single layer more easily, activate the Layers panel and hold theOption key down while you click the little eye icon of the layer you want to work on. All other layers in the document will be turned off. When you’re done, simply Option click the same eye icon of the active layer again to make the remaining layers visible.
Adobe Illustrator
Adobe Illustrator offers a simple tool to quickly apply colors, strokes, fills, effects, change fonts, and more to every item on a layer at once. The Target icon, the little round icon displayed at the far right of each individual layer in the Layers panel, is used to select every item on the layer. Click the circular Target icon, then apply a stroke, change a color, or apply a style to all the objects on the layer. This can be particularly useful if you organize your Illustrator documents as I do, putting all type on separate layers, backgrounds on another layer, etc.
Adobe Photoshop
When you have a multi-layered Photoshop document and for whatever reason you want to save each layer as a separate document, it’s quite easy to do – and requires no tedious cut & paste commands. 
Go to File>Scripts>Export Layers to Files. When the dialog box appears, you’ll have several options available including where you want to save the files, and a file name prefix. You can also choose from a number of file formats to save the document as, including JPG, PSD, PDF, TIF and more. Each format offers a few options as well.