I'm in the same boat. I've got a late 2013 iMac 27" with Mavericks. I've tired everything reset SMC, etc. disabled sleep, cleared out the sleep cache, etc. nothing seems to work. I've two ASUS 23" connected via HDMI -> Thunderbolt and when the system goes to sleep, and attempt to wake it up, either the system goes to all black screens or the primary iMac monitor turns on and one of the two ASUS monitors turn on but, the system is non-responsive. The only way to get the systme back is a hard shutdown via power button, reboot and everything comes backup without issue. There have been other times when unplugging one of the thunderbolt cables reinitilizing everything but, that is unacceptable to me.
At this point, I'm using the "command, option, eject" to power off the monitors when I'm away from the computer. I've also disable sleep, and hard drive sleep. Tested this configuration last night, and the system was responsive this morning to waking up the monitors. I'm going to continue to test for the next few days and see if this method proves to be realible.
Question, has anyone tired a DVI -> Thunderbolt connection and have had better results? Been thinking about purchasing DVI -> Thunderbolt and see if this fixes the issue, and maybe, this is a HDMI issue only. Know Apple monitors the boards, but figured I'd throw my name in the hat with everyone else. Hope Apple will investigate, and find a solution. However, my research tells me this has been an on-going issue with Thunderbolt for sometime.