Difficulty uninstalling modules that define own entity types

Not sure - never seen that. Could it be that your memory limit is causing some class of the Entity API not to load properly? Any chance you can up the memory limit during install? (Remember to leave the Commerce module itself installed until the very end.)

Reporting the same problem here. Works fine on my localhost (MAMP with php5.3). But on my dev server (nginx with php5-fpm for php5.3), I get the same fatal error and can't recover from it. Memory limit of 128M, so I don't think that's the problem.

Found a fix, at least. Line 115 is in Entity's create function. Not clear why it should be being called, but it's an if statement that includes the offending entityKey reference. I commented out the offending if statement (and the relevant close brace for it), and the site works fine again. Restore the module to vanilla, and the site stays working.

I guess Entity is trying to do something based on a cached list of entities... and when it tries to create the relevant entities for the recently-disabled module, it borks because the necessary variables aren't there.

Same here, comment out 115-117 seems to fix the issue, but when rollback to previous backup and uncomment it still generate those errors.

This is either a Rules or an Entity API issue.
This is how it showed up on my installation, didn't have time to test it out more:

1. Enable rules and entity modules
2. Enable a module that defines an entity type via hook_entity_info
3. Create a rule action that creates a defined entity
4. Uninstall the module from step 2
5. Try invoking the rule action from step 3

Please provide more details of what happens with the rule. Does the patch linked at #1325126: uninstallation troubles due to outdated entity info help?

I was trying to disable the message module and got the error:
"Fatal error: Class 'MessageTypeUIController' not found in /home/stashbash/public_html/sites/all/modules/entity/entity.module on 937"

I read somewhere that upgrading to drupal 7.12 would help with this issue so i did just that.

After upgrading i proceeded to disable the message module but unfortunately a new error showed up:
"Fatal error: Call to undefined method EntityValueWrapper::entityKey() in /home/stashbash/public_html/sites/all/modules/rules/modules/entity.eval.inc on line 115"

Any leads on how i can solve this problem?

I read somewhere that upgrading to drupal 7.12 would help with this issue so i did just that.

After upgrading i proceeded to disable the message module but unfortunately a new error showed up