It's been covered a lot in the past, on this forum and others, though the forum search results are a bit sporadic and overwhelming... so in order of performance and preference:
1. Mugen EK9 kit
2. Comptech/CT engineering icebox
3. OEM DC2 with DIY Cold air feed and quality aftermarket filter (very close to the Comptech/CT engineering icebox)
You can also construct a full custom kit with tubing, velocity stacks(2), a quality filter and an enclosure. You'll want the tubing going into the enclosure to be larger than the tubing going from the enclosure to throttle body. This effectively replicates a short ram instead of a long ram for better low and mid range gains, and only slightly less top end gain.
Personally I opted for the Mugen kit. It has the largest air intake and enclosure volume and I like the looks of it best. When I purchased my EK9 there was a cheap aluminum short ram on it. I changed the filter to a nice K&N that I already had and ran that for a while. Then I went with the Mugen kit and an aluminum intake tube(as I never had the OEM). The short ram was loud and aggressive sounding but there was a noticeable improvement after going to the Mugen kit. The car ran smoother and had better throttle response and power.
Btw, I haven't looked recently but when I purchased mine this was the least expensive place for a new Mugen kit:
http://www.rhdjapan.com/mugen-air-cleaner-and-box-civic-type-r-ek9.html