I'll describe some modifications that I've made on a Boss CS-3 pedal in order to improve it - hopefully it'll be of good use!
Some of the main problems that a stock CS-3 has are a huge amount of hiss and an audible "thinning" of the sound. Also, the highs are relatively "sterile". Most of my mods were dedicated to solving these problems.
I've recently acquired another CS-3, and this revision has a THAT2189LC instead of THAT2159 which my old CS-3 has. (I'll leave out the THAT2159 revision mods out of this text.) Those two THAT chips should be virtually identical, however the THAT2189LC/equipped model had a bit more hiss and a bit less sustain, but also more "musical" sound altogether.
I alwazs stress the need for a good power-supply, since the power-supply can transfer a lot of "impurities" in the sound. Therefore I've replaced all of the resistors which transfer the current to active elements with metal-film equivalents, as they have significantly less noise level. I've switched R3, R25, R26, R27, R28, R2 and R7 on the main board and R1, R2, R3 and R4 on the potentiometer-board with metal films of the same value (nota bene, this THAT2189LC revision has a 3K9 for R4, and 1K5 for a R7). I've also replaced aluminium-electrolytic caps with tantalum caps, so that C1 is now 47uF/25V, and C3 is now 47uF/16V. These changes have drastically lowered the noise-level and allowed more radical sustain.
Eventually I've replaced C5 (originally a 560pF ceramic cap) in the IC2b's feedback-loop with a multi-layered 680pF cap. I suppose it would be even better if I've used a Silver Mica dielectric cap, however I didn't have any available at the time. These changes have produced a warmer, more "musical" tone, especially in highs. One could use a 820pF for a C5, however the higs would then seem too "soft".
You could listen to a sound-sample here:
http://www.box.net/shared/ujglu5sw08 (Intro is clean guitar)
Power supply: AC/DC converter 9V.