what year of prelude do you have. the 4th gen S/Si can upgrade to VTEC 11" rotors and use several different calipers from heavier honda models for superior braking with factory parts.

u will want:
93-96 VTEC rotors

several caliper choices:
93-96 VTEC calipers w/brackets
97-01 VTEC calipers w/brackets
94 ish Legend GS+ Dual Piston calipers w/brackets
94 ish NSX Dual Piston calipers w/brackets

when i did this upgrade i also used earls SS lines to finish it off nice.
u can get quality remaned calipers for good prices at www.rockauto.com
i ended up spending about the same amount as doing a complete stock brake overhaul, and the performance is very noticeable.

as far as 5th gen goes, u are looking at aftermarket for bigger rotors etc.

~kris