After having frequent crashes on my multisite (which only has about 12 users with domain-mapped sites) I have determined the problem is that mysql keeps crashing.
I have my WP memory limit set to 128M and it looks like the error log shows some problems related to that. I've googled these errors like crazy but can't seem to find the right advice as to what to change in my mysql settings.
150125 14:19:05 InnoDB: Initializing buffer pool, size = 128.0M InnoDB: mmap(137363456 bytes) failed; errno 12 150125 14:19:05 InnoDB: Completed initialization of buffer pool 150125 14:19:05 InnoDB: Fatal error: cannot allocate memory for the buffer pool 150125 14:19:05 [ERROR] Plugin 'InnoDB' init function returned error. 150125 14:19:05 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed. 150125 14:19:05 [ERROR] Unknown/unsupported storage engine: InnoDB 150125 14:19:05 [ERROR] Aborting