Okay, let’s get some things out on the table first. I want to try and keep this post informational. The last one got carried away with questions. Questions should either be researched or posted so you can get addressed and people don’t miss informational posts thinking it is all questions and answers now. Thank you for understanding. One more note: When I reference the SI I mean the 5th Generation Hatchback not the 1999-2000 Coupe.
First off I want to provide some information as to why Single Overhead Cam (SOHC). Because every almost every Civic out there has or had one to begin with and not everyone has the money (or patience) to buy a Dual Overhead Cam (DOHC) changeover. Sure, you may end up spending just as much money in the long run however, you will get to do things every now and then instead of just saving money. So, let’s get started shall we?

Intake: First things first. Allow the engine to breath, after all engines are nothing but big air pumps. To start off, we look at the filter and piping. AEM Cold Air Intake’s (CAI) are nice, common and even California smog legal. The great thing about the CAI’s is that they don’t suck in hot air from the engine bay. RSX’s have been dynometer (dyno for short) proven at +20 whp with CAI as apposed to the 5-8 wheel horsepower (whp) with a “short ram” design. There have been dyno sheets that show a 3" piping makes great power, the Integra Type R (ITR) CAI will fit on Civics and is 3” unlike the EX/SI CAI, which is 2.5”.
Next inline for the intake is the throttle body. This is more of a throttle response upgrade than a horsepower upgrade. They simply allow the engine to get its full breath of air faster because of the larger opening. Almost all Honda throttle bodies will bolt onto the D series intake manifolds, and will fit to the intake manifold with a little port matching. The VTEC B series and B20 (CRV) throttle bodies are all 60mm in size. Except for the ITR, which is 62mm. The H22 is also a 60mm throttle body. While the Civic, gets a puny 56mm.
Don’t forget about changing from electronic fuel injection (EFI) to carburetors. There are a few ways to do this, and it is a novel on it’s own. However, it takes makes fueling and ignition easier because carbs have been around for such a long time that there is an insane amount of knowledge about them.
Next, we come to the intake manifold. NOTE: This will not work for the D17's. Honda had the bright idea to make it a returnless fuel system. For that you want the D16Y8, often referred to as the Type R manifold for the D series. It has short, fat runners and a large chamber to allow the air to distribute to each cylinder properly. Also, for the non-vtec guys out there, it has the common horizontal throttle body, which will allow you to use the larger CAI's.
Lastly, don’t forget that heat here is a performance killer. In warmer climates you can remove your throttle body and Idle Air Control Valve (IACV) “coolant” lines to keep the heated coolant from them. Also, you can invest in a Hondata intake manifold gasket. It is designed (and proven) to protect the intake manifold heat soak.

Exhaust: Lets start off with the exhaust manifold (header). There is no OEM exhaust manifold out there that doesn't need work. The HF (all Civics other than the EX and SI) exhaust manifold can be modified to add a turbo. Then you don’t need to spend the extra money on a turbo manifold. But, for those of you who want to stay naturally aspirated (or don't have the money for a turbo) a used aftermarket manifold for the EX is where you want to go. There are a lot of people out there who by the time they can swap have already put a header on there D series and now need to sell it. You will have to relocate your catalytic converter under the car to use this header configuration (which happens to be illegal in some states). There is two different designs for a header. The 4-2-1 (or Tri-Y) and the 4-1. It is said that the 4-1 costs you low end torque to give you more power up top. However, if you follow this link http://www.automotiveperformanceengi...om/header.html you will see that some 4-1's have more low and mid then the 4-2-1's. Header desgins are so good that this is more a preference thing IMO. One advantage of the 4-2-1's is that you can remove the lower half when you need to pull the oil pan. Instead of pulling the entire header.
Following the exhaust stream out, we come to the Catalytic converter. Unless yours is old, don't worry about it. For those of you who can afford to upgrade the cat, tests have shown that a 3" free flowing cat has almost flown as much air as a 3" test pipe. In fact some people were shocked at how well a free flowing cat works (and it's legal). Or go with the 10.00 test pipe from Home Depot (NOTE: Test pipes are not smog legal and you face a $3,000 fine). That's right, people have even made there own test pipes with minimal effort.
After the catalytic converter, it’s the “Cat-back”. Most people recommend using a 2.25" sized exhaust for the little 1.6L. And a lot of the aftermarket exhausts are 60mm
or 2.3 inches. I agree that they should be at least 60mm. But, you also want to make sure you get mandrel bent piping and strait through designs on both the resonator (if you have one) and the muffler. If you don't get the strait through designs, you will loose power, it's that simple. However, with straight through designs also comes noise. A good compromise has been the Apexi World Sport (WS) cat-back.
Transmission/Flywheel/Clutch. Remember this, the shorter the gears the better. It is easier for the engine to push/pull the car. MistaBone's link. http://home.cinci.rr.com/mistab0ne/tranny.html</A> The VTEC engines have always had the shortest gears and it is a bolt on part. The 96-00 trannies will bolt on a 92-95 Civic. Also consider a ZC tranny with a SI final drive. For you cable tranny guys, there are the Hasport kits that convert your Cable to a Hydro. And, SRR offers a 4.7 and a 4.9 final drive for the D series transmissions. See <A HREF="http://www.aj-racing.com" TARGET="_blank">http://www.aj-racing.com about those. HX/VX/CX owners, upgrading the tranny should be the first thing you do. HUGE difference.
Once you get the shorter geared tranny or already have one, a limited slip differential is the second biggest thing to have on a D series. The performance improvement is profound. I recommend Quaife because it has gears, not a clutch and it comes with an unlimited lifetime warranty.
A lighter flywheel is also a recommendation. Not only do the increase throttle response, they “free up” horsepower by decreasing rotational mass. The aftermarket offers weights varying from 8.5 lbs to 15. You can shave your existing flywheel to no less than 13 lbs. However, this is a controversial issue and if you search will discover how everyone feels about it and the dangers that can come with it.
The clutch. Man, talk about a weak POS, the stock one simply sucks. With even stock tires your clutch will start to give out while doing a warm up burn out at the strip. There is no doubt, you have to upgrade this part or suffer the sliding shift every time you drive hard.

Engine: Well, where the hell do we start? The motor mounts all have gaps in them. Filling them with window cement is a poor mans way to get some “solid” mounts. Okay, now that you got that sucker still, lets increase some power.
On a naturally aspirated engine there are # things you can do. 1. Up the compression. 2. Increase the displacement. And 3. Add more aggressive cams.
One way to up the compression is to mill the head. It is very important for you to not remove more than .30. If you do, you risk timing issues because the timing belt is going to be shortened and you will risk jumping teeth. You can also get thinner head gaskets, the Y8 is cheap and is the thinnest metal OEM head gasket that you can get.
Now that we have covered some inexpensive increases, lets go to pistons. The 1988-1989 D16A1 Engine came with some really high dome pistons. They cost around 30 dollars each from the Acura dealer as well, and will increase your compression ratio as follows:
d16a1 pistons (stock bore) in the following with a y8/z6 metal headgasket(no mill):
d16a6= 11.08: 1 compression
d16z6= 12.03: 1 compression
d16y8= 12.61: 1 compression