Render Queues in After Effects are great: they're easy to set up, there's a lot of great options to them, and there's a lot of things the engineers at Adobe have put in to streamline the entire process, such as things like remembering the last folder used for a previously queued render. However, to save out commonly used render queues is not directly possible directly in After Effects itself. It is possible, with aerender command line rendering. 

There are many benefits to command line rendering, one is that After Effects remains useable in the foreground while it's background process does the number crunching for you. It is much quicker than regular renders, with some claiming 40% faster render times. The thing I've found the greatest is that you can save out render queues in text files then simply load them up in terminal. You can even save out multiple render queue texts, and then queue them all in another text, then queue it up in Terminal. The possibilities are almost endless. Best of all, if you need to re-render in a pinch and don't want to waste time setting up the queue again, just load up the command line and you've got an easy way to re-render out new data.

There one downside I have found to this method, is that composition/footage names are not unique in After Effect projects. If you have multiple compositions with the same name, aerender will take the first one it finds in it's stack. This gives greater incentive to properly name assets, which does become difficult when you're constantly pre-comping everything and get lazy with the naming methodology.

So, here's what you need to know:

1.  Open Terminal and either navigate to your Adobe After Effects folder in the Applications folder, or simply use a direct command to a program called aerender.

##This will Navigate To the After Effects Folder, Replace [CS5] with your version.##
cd /Applications/Adobe\ After\ Effects\ [CS5]/

2. Then use this command to start a render:

./aerender -project path/To/AEFile.aep -comp "composition name" -RStemplate "Best Settings" -OMtemplate "PNG SEQ (STRAIGHT)" -output path/to/RenderOutput_[#####].png

As you can see there are multiple flags being set. There are more that you can use, but these can get you started.

-project is the path to your project file.

-comp is the composition's name

-RStemplate is the render template you wish to use. These can be your own templates you've created for the project. 

-OMtemplate is the output media type template. These can be your own templates. I've used a PNG Sequence template I've specifically created for this project. 

-output is the output path to the final render. Because this is a PNG sequence output, I've specifically used the proper [#####] counting format that AE uses in it's render queue. This can be any format you wish, I've generally kept it the same.

3. Then, getting a little more advanced, you can set up the same data in a plain-text file. I've set mine up like so:

cd /Applications/Adobe\ After\ Effects\ CS5 

./aerender -project /Users/Me/Project.aep -comp "my_awesome_comp1" -RStemplate "Best Settings" -OMtemplate "PNG SEQ (STRAIGHT)" -output ~/Desktop/render/myAwesomeComp1_[#####].png
./aerender -project /Users/Me/Project.aep -comp "my_awesome_comp2" -RStemplate "Best Settings" -OMtemplate "PNG SEQ (STRAIGHT)" -output ~/Desktop/render/myAwesomeComp2_[#####].png
./aerender -project /Users/Me/Project.aep -comp "my_awesome_comp3" -RStemplate "Best Settings" -OMtemplate "PNG SEQ (STRAIGHT)" -output ~/Desktop/render/myAwesomeComp3[#####].png

You might notice that I have used ./aerender. I've noticed that by typing aerender even when in the directory tends to not work. When I figure that out, I shall update this tutorial. ./aerender works for now. 

You can also use a direct path to aeRender, such as: 

/Applications/Adobe\ After\ Effects\ CS5/aerender -project [...]

I just found that was a bit too labour intensive and made it look messy. Feel free to use this method if you do not wish to navigate directly to the folder.

4. To actually run the text file in terminal, you can simply use this method:

source path/To/TextFileRender.txt

Terminal will then run all the commands you have listed in the text file. 

If you're super adventurous and wish to keep queues separated for various reasons, you can set up master queue files to source all the text files that hold the commands. This is super handy when you know how you want to separate out your render system.

source path/To/TextFileRender1.txt
source path/To/TextFileRender2.txt

Then just source that file in Terminal and you've got yourself a pretty easy to use render queue. 

There is much to be said about Render Queues for After Effects. A lot of the time you've got compositions within compositions that sometimes you need to render out separately. Knowing now that all those things can be streamlined in text files is a great help for the common After Effects user. No more long histories of render queues inside of After Effects to maintain and take care of in case a re-render is needed. As well, I've noticed significant speed improvements when utilizing aerender. 

Further information can be found here at the Adobe website and a little bit of Terminal learning, you can be on your way to a streamlined render method with After Effects.