If, like me, you get annoyed at always fiddling with the export settings in After Effects, you should take the time to set up some templates and change the defaults.
In the Render Queue window, set up your Output Module with your desired default settings. I typically use a TIFF sequence with alpha channel. Once it's set up, click the drop-down arrow next to Output Module and choose the last option: "Make Template…" You'll get a window with two boxes in it labeled "Defaults" and "Settings."
Give your template a name in the Settings Name window, then in the Defaults box, choose the template as your Movie Default. After Effects will now use those settings as the default whenever you export a Comp.
Now, if you've ever tried to use a TIFF sequence from After Effects as an image plane in Maya, you may have had some difficulty getting it to work. AE's default naming convention is fileName_####.tiff. Maya doesn't like that underscore; it only understands an image sequence if the frame numbers are delineated with a period, like so: fileName.####.tiff.
Click the drop-down arrow next to Output To: in the Render Queue, and choose "Custom…" You'll get a window called File Name Templates. Set up the Template like this: [compName].[#####].[fileExtension] and check the "Default" box.
Now, whenever you set up a TIFF sequence, you'll get file names that Maya can use.
edit: I've been doing some research on file formats (post on that topic coming soon), and I've decided to stop working in tiff. I've had problems with it in the past where I couldn't open an image I created with a PC on a Mac, or I couldn't read tiff sequences created by Nuke in Premiere (don't use DEFLATE compression—Premiere can't read it). Tiff certainly has some useful features, but there are so many different flavors that compatibility becomes an issue. Instead, I intend to switch to Targa for wider compatibility or OpenEXR if I need high bit depth and/or more than four channels. The only gotcha to that is that if you need transparency with Targa, you need to tell AE to render 32-bit files (four 8-bit channels). I don't know why the Targa export specifies bits per pixel when everything else is in bits per channel, but there you go.