I like @joho68's idea of a META key. Here's some other ideas:

CTRL + R

• Reply to previous message: CTRL + R, R
• Reply to one above previous message: CTRL + R, 1
• Reply to two above previous message: CTRL + R, 2
• ... etc through 10 (0; of course)
• The 11th will have to be clicked.

Note: second key press is without letting go of CTRL.
Note: I realize now that CTRL + R is a bit ... occupied ...

Slash Command

Additionally, replying to the previous message may be as easy as /r like is available in many video game chat systems. For example:

/r That's a great idea! I'll get started right away.

Indicator

Some sort of indicator (like what shows up when you type the forward slash (/) would be nice. This indicator would show the message your replying to ... so you know you targetted the right message.