My venerable MOTU 2408 bit the bullet this weekend so I went out and got a brand new Apollo Firewire interface to replace it. After muttering the correct runes over the new interface and recommended FW800 card, I got it working. Occasionally I see the perf meters in Sonar spike with a corresponding audio dropout. I don't see this using any other audio application. The dropout is brief, on the order of milliseconds but noticeable, no pops or anything, just no sound. It doesn't seem to affect the bounced track, when I play a bounce in WMP it sounds fine. I'm using ASIO and have tried setting the buffering / latency to max with no improvement.
I use an external mixer for monitoring so latency isn't an issue for me, but the dropouts are pretty annoying.
Any ideas?

Audio dropouts........the first thing that comes to mind is DPC latency. Have you checked your DPC latency lately?
But then, if DPC is really an issue then it would probably happen in other DAW hosts as well. Could be that SONAR is more sensitive towards it? I have an ASUS Z87 Deluxe/Quad MB/i7 4770K/Apollo Quad system. I did go into the BIOS and disable all non-DAW related devices (HD Audio, Wireless, unused USB/LAN ports, etc...) and that brought my DPC latency down to near nil. I've kept my Intel LAN port enabled so I  can download updates over my hardline(SONAR, Windows and other DAW related stuff from trusted websites), but I do all of my web surfing on another dedicated computer. Are these audio dropouts during recording and/or playback? You are using the recommended Texas Instruments FW800 drivers with the Apollo correct and you are running Win 7 "sp1"?
 
http://www.resplendence.com/latencymon_whatsnew
 
Cheers,
 
Billy Buck