I have a MMA 7660 3-axis Accelerometer and, using the library available here (http://www.timzaman.com/?p=1089), am able to read the x,y and z values from the accelerometer in the Arduino terminal.

Using the [comport] object in Pure Data (Pd), I am also able to get these values coming in there. However, in Pd they come in as a single stream of numbers of all 3 axes combined - the unpack object has no effect. Does anyone know how I might go about unpacking the separate x,y and z values from this stream?

I'm not very deep into that, but I would prefer osc-style messeges.
Just found that, and looks promising:
http://cnmat.berkeley.edu/oscuino
edit:
http://cnmat.berkeley.edu/book/export/html/11389

I'm replying quite late to this, but I'm doing it anyway.
Are you using the Arudino sketch provided by the website you're mentioning?
What happens in that sketch is that it does send three pairs of values, but the last one is sent with the println method which attaches the carriage return and line feed to the transferred string.
What you need to do is probably this:

[comport]
|
[sel 10 13] <- these are the line feed and carriage return ASCII values
| |
| ____[repack 9] <- repack should probably be 9 cause you're gonna get

a three digit number (e.g. 100 will be 49 48 48 (this is ASCII)
|
[unpack f f f f f f f f f]

Still, receiving data in ASCII is quite cumbersome (at least for me), cause after [unpack] you have to figure out what number these ASCII values represent. You'd be better off using the Serial.write method in Arduino, but that's only 8bit, so you won't be getting values higher that 255 (if it goes higher it wraps around to 0). If you're still having trouble I'll send you a sketch and a patch that read an accelerometer (without using the library you're mentioning though).