Should I take out my AR-16 tube pre amp from HT?

The only way things could potentially sound any better for 2 channel CD sources, VCR, etc, would be if the DAC's in your CD player(do you have one?..or are you only using your DVD player for CD's?) aren't so good as the ones in your Sunfire! If that's the case, it's possible your processing through the Sunfire is giving overall superior resolution and refinement of sound over what your CD player is feeding your preamp when connected straight to your AR 16(LS16?). If you are talking about the LS16 AR preamp with dirrect passthrough, and you do have a quality CD player, the sound is going to be potentially better for analog sources if you connect dirrectly through the AR preamp! So it depends. You do however need to connect all digital connections for DD/DTS through your sunfire for best sound, rather than processing inside, say your DVD player, and not using a pre/pro. It never sounds as good that way.
I used to use the Audio Research LS16 with dirrect bypass for 2 channel/HT dubties, and it sounded fantastic using the "bypass" when using an outboard pre/pro for movie watching. I'd simply use my beter CD player's analog outs to the LS16, bypassing the pre/pro. I also connected my tuner and vCR to for 2 channel listening this way. The only connection I had to the pre/pro was the digital out of my DVD player for movies.
I don't know all the components, connection, or speakers and such you have in your system, so results could vary.
Hope this helps. Never the less, the LS16 is a better preamp potentially than the Sunfire by far! Good luck

My preamp is the Audio Research LS 16 and my CD player is the Sony S9000es. When I played the two together it gave me a "leaner" sound. However, I preferred the "warmer" and all around sound when the CD player was hooked to the Sunfire and the LS 16 running on "pass through".

Two questions arise. Is the Sunfire "upsampling" my CD signal? And, is the LS 16 doing anything to my signal at all when in "pass through" mode?

I suspect yes to the former but I'm not clear about the latter.

I love my LS 16 but if it's not serving any function in this set up, I'll pull it and put it away to save the tubes.

Thanks for caring.

The sunfire is a very good two channel pre (I have one) so it could be that it does sound better. As Foreverhifi say, you need to run your cdp analog outs to your LS-16 and leave the sunfire out of the picture to compare between the two. If the sunfire still sounds more to your taste then get rid of the AR-16 and if not then keep it. The bypass in the AR-16 is for movies so that you can pass your pre/pro signal and still use outboard two channel pre for music.

Blame it on synergy or file under "Go figger" Dept.

I took the LS 16 out of my set up and my soundstage went flat. My sound lost all it's "fullness" - no body in the mid ranges and under. Needless to say, I quickly restored the equipment arrangement.

Maybe my stereo signal enjoys the "extra" traveling through the Monster and MIT 3 interconnects through the LS 16's by pass because when I connected my Sony S9000ES DVD/CD player directly to the Sunfire and had the Sunfire wired directly to the amp, my sound went "flat".

Ahh, the mysteries and wonders of our obessions.