HI Eric,
There is a setting in Messages on the Mac in the View Menu > Sort Conversations (By Time or Manually)
but this only effects the way they move to to the top in the left hand column if you have more than one chat going on.
It does not effect the order or IMs or iMessages.
IMs (from AIM or Jabber Buddies) do not seem to suffer with this issue and those messages (IMs) are Time Stamped as well.
9:19 PM Friday; December 7, 2012
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.2)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad
"Limit the Logs to the Bits above Binary Images." No, Seriously