There was a member here who cut the front intake holes out to improve upon the restrictive front grille- search for posts by 996GT2. The high impedence of the front grille is one main problem cooling-wise with the WaveMaster. Note that the front aluminum is VERY thick, and you have to take care not to damage the support pillars for the aluminum piece that hides the grille.
I decided that instead of going through the trouble of cutting out the front grille, to cut out a 120mm hole on the side panel right over the CPU heatsink area for passive intake (no fan). This alone dropped my temps by about 4C. It would be a good idea to filter the hole as well. I actually experimented with a side intake fan, but found that there was no improvement in CPU temps with the fan, and the mobo temp actually increased 1-2C.
I removed the top USB port because I never used it, and the cables made for messy wiring. However, my experience with a blowhole in this case has been that it makes no difference whatsoever, while contributing to noise and increasing the possibility that something will fall into the hole and fry the system. I now have the mesh fan holder sans fan, and actually keep the mesh covered with a book to both prevent stuff from going in, as well as to dampen noise coming out. If I were to do it again, I would probably just have removed the cables and connectors from the top metal plate and left it in as is.
I added an 80-120mm fan adaptor to the outside of the rear exhaust hole and coupled it with a GlobalWin 120x25mm fan. The fan wire was put through a PCI slot where I removed the cover. The GlobalWin, despite being a ball bearing fan, undervolts on PWM very gracefully. Slapping on an 80-120mm adaptor and the GlobalWin to the rear dropped my CPU temps by at least 3C under full load, and was much quieter. You may find that the adaptor interferes slightly with removal of the side panels, but you should be able to get around that.
I currently use the front intake fans mainly as a mechanism to cool my HDD; I am sure some air does come in through the front grille, but the side 120mm hole is the primary intake mechanism; I have an SI-120 cooling my processor, and the fan on the heatsink is positioned right over the 120mm hole, allowing efficient passive intake through the hole. I am not sure how well this would work with tower-style heatsinks.
If you do not want to use any 80mm fans in the system at all, it is possible to mount 92mm fans for front intake. You cannot screw them in, but the front mounting bracket will allow you to slide a 92mm frame in; mount the fans with double-sided tape or velcro, or some other adhesive. I currently use Arctic Cooling 92x25mm fans, and they are OK, although nothing special; they also lack RPM monitoring, but they are cheap and are rated for a long lifetime. The do not have any ball bearing clicking when undervolted via PWM, which is a plus. There is some motor hum, but as long as they are run at low volts, it is not too bad.
I would strongly suggest you control the fans with a fan controller; the CoolerMaster Aerogate 3 is a good choice for the WaveMaster, as many controllers that use knobs will not work with the WaveMaster's front door; the Aerogate has been on sale at SVC for $8, and at that price, simply cannot be beat.
SVC also has 80x25mm GlobalWin fans; if the 80mm model is anything like the 120mm, it would be a solid choice if you wanted to use 80mm for front intakes, or were set on having a blowhole fan.
80-120mm fan adaptor
GlobalWin 120x25mm fan for rear exhaust
Aerogate 3 fan controller/temp monitor
Arctic Cooling 92x25mm fans