Script to create video in standard format? I've been making videos (episodes) for my YouTube channel. They are all in a standard format with an intro which has the episode # and title, then the clips fade in always using the same simple cross-fade. I'm putting it all together using After Effects CS6. It seems to be too time consuming to manually trim/align the clips and then apply the transitions.

The first thing I do is watch my source content and note the in/out times for all of the clips (could be one or more in/out per clip). Then I mark certain things like "speed up 4x" or "no audio", etc. I wonder if there's a way I can write a script and then have the video be produced for me, quickly. I'd need to supply some values  for some variables, such as episode # and name, and then the in/out/etc. for each clip.

What tools exist that would allow me to create the final video from a "script"?

PS: I'm a software engineer so I'm sure I could just write a program to do this for me, but I'm sure it already exists!
I'm not aware of any software that does what you are looking for.  The workflow doesn't really fit within a typical post-production workflow, so there isn't really a reason for it.  You can find software that will do things like adding the beginning and ending leads to a video based on meta data, so doing the titles automatically should be possible.  However, actually making automated edits based on timestamps is fairly non-typical.

Generally, the clips are cut in as they are reviewed if you are reviewing that way.  You can watch a clip, set an in and out point and then send it to the timeline.  This way you document the edits and build the sequence at the same time.

Your best bet would probably be to use software for making EDLs (editing decision lists).  If you can produce an EDL with the cuts you have defined in your "script" then software that can process EDLs (such as Premiere) should be able to make use of them.  Normally EDLs are used for transitioning between different editing systems, so it should be possible to modify or create your own EDL fairly easily.