I've got a '98 Civic DX and here's what I did:
AEM Short Ram Intake, DC Sports 4-2-1 header, 2.5'' cat-back exhaust with a Jackson Racing High Flow Cat, Mini-me Head Swap (putting an EX head on you're stock block, gives you SOHC Vtec but doesn't really do much for power), ACT HDSS Clutch with an XACT 10lb. flywheel, OBD-1 conversion with a Skunk2 chip and tuned using Crome. yeah it costs money but it's fun to build up a D-series motor. I would suggest doing the basic i/h/e mods first and then going from there. For some real increase in power save up for a turbo. You can run 6-7 psi on the stock block. Oh, and I keep up with DOHC motors