What combo do you have? Screw what other people use... use the right one for your combo.
The HPS is intended for NPI/PI headed cars that want to spin to about 5500rpm (PI heads) to 6100rpm (TFS heads). For mostly any NA 5.4L mustang application this is the ticket for now. It'll flow with TFS heads and we've seen 375rwhp through it on stock TFS heads and a nice cam. Fits under a stock hood and bolts right up. 4.6 Fuel rails usually bolt up just fine.
I have a 5.4 with port matched heads and Comp XE270 cams, 10.5:1 and longtubes. I use the HPS intake.
MMR's solution is ONLY for blower/turbo cars and I think it's a crappy hack of a solution with too much of a hood clearance problem and a fuel rail compatibility problem (uses Lightning rails).
Logan could make one of theirs which is totally pimp but it's unthinkably expensive and has its own hood clearance problems and more fuel rail issues.
Edelbrock Victor Jr. 4.6 and adapter plates. Crap solution. Wrecks fuel delivery. Please don't do this.
FWIW, MHS (modularheadshop) is putting the finishing touches on a 5.4 2v single plane type intake that is for cars with TFS heads (stock or ported) or heavily ported PI heads and cams over 230deg duration. It's for those guys that want a 6500rpm+ shift point. You can see early CAD drawings of it at
http://www.modularheadshop.com/Articles/54%20intake.htm
Oh... BTW REALLY IMPORTANT! If you want a HPS 5.4 intake, you better get it now. He's got a batch ready to ship and he doesn't make them very often. Most of this run is spoken for, get yours while you can.