Say I have 100 commits in my branch that I've been working on for 3 weeks. Occasionally (every day, really) I pull from origin/master and merge it into my branch.
How could I (easily) go about squashing all of my commits into one commit without messing up history? If I squash all of my commits into one somehow, would I destroy the merged origin/master pulls when my pull request gets moved into origin/master?
"Squashing" and "preserving history" are approximately direct opposites in terminology.
If you mean that you want to make a single commit that includes only your changes and not the ones from upstream master, you would probably want to rebase onto origin/master and then squash from there. You could do all of this from a single invocation of interactive rebase:
git fetch origin
git rebase -i origin/master
and then change all of the lines after the first from pick to squash.