[Phanx]

I don't have time to look over it in detail at the moment, but I did notice:

local function HookHandler(self, event, func)
        self:HookScript(event, func)
end

for i = 1, NUM_CHAT_WINDOWS do
    local chatframe = _G["ChatFrame" .. i]
    HookHandler(chatframe, "OnHyperLinkEnter", MouseHoverToolTip_Show)
    HookHandler(chatframe, "OnHyperLinkLeave", MouseHoverToolTip_Hide)
end

What is the purpose of the HookHandler script? Why spend memory and CPU time wrapping :HookScript in a second function like that when you can just call it directly:

for i = 1, NUM_CHAT_WINDOWS do
    local chatframe = _G["ChatFrame" .. i]
    chatframe:HookScript("OnHyperLinkEnter", MouseHoverToolTip_Show)
    chatframe:HookScript("OnHyperLinkLeave", MouseHoverToolTip_Hide)
end