I've noticed a lot of rips I have for whatever stupid reason have the tracks loop an extra time. This is annoying because the songs are taking up twice as much space as they should and I never go "Wow, I want to hear the same song twice in a row every time!".

Is there a program that I can just feed songs into and it'll automatically just halve the songs or do I have to tediously go through every track in Audacity?

Here try this app rather than using Audacity: mp3DirectCut (http://mpesch3.de1.cc/mp3dc.html)
It can slice/splice mp3 files directly with no decompressing/recompressing.

I convert tracks to wave using Easy CD-DA (or Winamp) and then I use Nero Wave Editor. I loop almost every album I have because I like triple loops instead of standard double loops.