Greg (yatzr) believes he's figured out the issue, Here's what I got from him via sitemail.
Good news! I'm pretty sure I got it figured out. Would've really struggled if it wasn't for Seble's clue - "The only change yesterday was swapping out our site analytics package."
The tools all use an old library called httpunit that hasn't been updated in 10 years. Literally any request to WIS was choking while trying to parse the html. On the hunch, I tried updating the httpunit source to strip out the bit about google analytics at the bottom of each page, and then it started parsing fine. I was able to get the game analyzer back up and running this way.
Why would the library choke on that bit about google analytics? ¯\_(O)_/¯ your guess is as good as mine.
I'll try to get new versions of the tools out tonight...then I'll have to do a fundraiser to buy my wife an apology gift for neglecting her this evening, haha.
And later
Here's the game analyzer
http://gdreports.com/tools/yatzr/yatzr_game_analyzer_1.9.5.jar
One important thing to note. I think the files I had backed up were for version 1.9.3. My changelog says 1.9.4 updated the following
"Version 1.9.4
Updated for new lines in the extended pbp. Now if it says the defense gets the first step or is starting to break through, then the Prsr is a 1. If it says the defense broke through, it's a 2."
I don't remember the exact details of what that change was, so I don't know if they are in this version. If not, and somebody else remembers what that was about, I can update it pretty easily.