Pyffi'd my Oblivion Meshes bsa, Shivering Isles Meshes bsa, Knights bsa, and Verona House bsa. Game crashes on transition from interior to exterior, fast travel to exterior, or from city to exterior. I've encountered this before, and thankfully backup my bsas before doing anything with them. Never had this problem with my old copy of the game, but with my GOTY copy (specifically from the Elder Scrolls Anthology) pyffi breaks my BSAs. Optimizer Textures is okay, though it crashes if I try to do Shivering Isles textures.

Any ideas what's going wrong? A little google research tells me this is a problem with pyffi and the GOTY edition specifically, can anyone tell me if there are any workarounds?

GOTY Edition refers to Oblivion and two other expansions right? I pyffied the BSAs and I don't experience any problems that you described. Well I do get random crashes from time to time but not like this. Are you using the latest supported python and Pyffi softwares? Refer to this guide here for detailed instructions: http://testg.wikidot.com/utilities:utilities#toc7

Yes, python and pyffi are both up to date.

It's probably something else that is causing the crash. I have the same GOTY Edition disc version and crash for my game is not that severe. It is quite stable but once in a while it would CTD. Check to make sure your order is according to BOSS or LOOT and also be sure to remake the bashed patch whenever you change anything in your load order.

If that does not help, remove all of the mods that are installed and start from vanilla. Install the mods one at a time to test the game. If it does not crash, add another mod and check again. Do continue on until you recognize the same issues as before. If necessary keep the current save files and create a test character. You can always restore the current state later.

If I pyffi my oblivion meshes, my game crashes when loading a non-city or non-interior cell.

If I replace my pyffi'd .bsa with the original, it stops crashing. It's definitely the pyffi