Good Intermediate Format for Combining Videos I have a bunch of PNG files in separate directories that I'll turn into videos with FFMPEG.  Say each clip will be a minute long.  I then want to stitch those together into a final video.  The final format can be anything YouTube accepts.  

So, I need a format that won't lose a lot of quality when the PNGs are encoded the first time, and that doesn't lose any quality when it's concatenated to other videos of the same format (some need to be re-encoded and some behave like UNIX's cat).  They will also each have their own audio tracks which need to stay lined up correctly.  So, do any audio formats have problems with this?  I can have them in any format.

Also, is there a way to set the video durration longer than then would be assumed?  Say I have 48 frames showing at 24 fps.  Could I have it make the video 3 seconds instead of 2; holding the last frame for a full second?
What you wish to do is somewhat convoluted. There is a path to achieving it in the 2 step process you propose, but I would just suggest creating a new folder where you copy all the input files and rename to form a continuous sequence.

Let's say you have 3 folders and the following files in them to be joined in that order

Folder A: a001.png, a002.png, a003.png, ...... a175.png

Folder B: b0001.png, b0002.png, b0003.png, ...... b1075.png

Folder C: c01.png, c02.png, c03.png, ...... c75.png

Also let's say you want to hold the last frame of B for 5 seconds

So, you rename a001-a175 to s0001-s0175; rename b0001-b1075 to s0176-1250; duplicate s1250 120 times (24fps x 5) and rename the copies s1251-s1370, and finally rename c01-c75 to s1371-s1445.

This method avoids issues of video generation loss. For audio, WAVE files of the correct length and order can be appended losslessy by FFmpeg and then converted+muxed with the output video.

Of course, I see from your history that you have access to Premiere Pro. The simplest way of all would be to load all PNGs and audio in the editor, assemble and take output.