Hi Chris,
I have an Emerald and a Mule on a Les Paul, the Emerald gives great harmonics (but so does the Riff Raff). I wanted the Thin Lizzy type of lead tone (from Still In Love With You), and can get that but much more besides. I also have VHII's on my PRS. This is more of the Santana sound (but before Smooth!), think Samba Pa Ti or Black Magic Woman.
I just got a custom wound, which is the new Riff Raff (I think this is correct - right Tim?), at fist with new strings I thought it was a little bright, but as soon as the strings settled in it was perfect. I have essentailly a Stormy Monday with Alnico IV in the neck and this combination is great. You can get the Peter Green sound with the 2 pickups (the Riff Raff is Alnico V), without needing to be out of phase, and without the resulting volume drop. I would really go for this if you want the old blues/rock tones. The only thing is that you will start to play with the volume controls a lot more. Besides BKP's usual trick of getting a great sound down to 1, the combinations now get different tones as you increase/decrease one against the other.
I also do love the Emerald/Mule combination too. The difference is perhaps that it is more a rock/blues setup than a blues/rock, if this makes any sense to you at all! But with my Marshall it is a tough choice because I can basically get any sound from both of them. I think there are perhaps more clean tones in the Riff Raff/Stormy Monday setup. The VHII's are more powerful in a way, but because they are on a PRS with the 5 way, it is harder to make a direct comparison. Your best bet might be to come to the Guitar show and have a listen.
Hope this helps a bit.
Phil