Of course, it goes without saying that the amp will lend it's own voice to the mix, but let's face it, mostly what it is doing is working with what is fed to it. I'll give you a real life scenario.
I recently completed a major overhaul of my system. My Klipsch Cornwall III's were fine, so they stayed. I bought a new Bob Carver Crimson 275 amp, and replaced my Vincent SV-237MK hybrid integrated amp with a Vincent SA-T7 tube pre amp even though I could have used the MK as a pre amp. Long story short, I didn't like the way it sounded. I put the MK back in the mix and got the sound I was looking for back. Both Vincent's are stellar pieces of equipment, and the 237MK is an excellent integrated amp. Where the difference came in was that the 237MK has a loudness switch, something that I use 90% of the time. So, in my particular setup, and with my preferences in sound, the pre amp made all the difference in the world.
Component set ups can be tricky because each piece brings it's own contribution to the party. Getting everyone to play nice together is a juggling act, but it can be quite rewarding when you get everything right. The down side is that it can be an expensive experiment to conduct. IMHO, the best way to approach it is to stick with a single manufacturer and chose pieces that were designed to be together.
