I've read that Audiocatalyst chops off some of the higher frequencies.

Not just Audiocatalyst, but pretty much every MP3 encoder out there. There is one exception. LAME claims to preserve the higher frequencies more accurately at high bit rates, and I'm evaluating LAME right now for use with my personal collection.

Does the encoding process chop off lower frequencies as well?

No. In theory, the lower a sound's frequency, the easier it is to data-compress accurately. I get great bass out of my Empeg, even on low-bitrate files.

Note that the Empeg's audio output circuits are EQ'd very "flat" by default, and the bass is not artificially boosted like it is on many car CD players. So the bass on the Empeg will start off sounding less pronounced than it is on the CD player it's replacing. Fortunately, the Empeg has an amazing equalizer that will let you dial in the exact settings you want for your car.

Keep in mind that I encode at 128 because when I compared recordings to VBR I either couldn't hear or didn't mind the difference, and I'm using as good computer speakers as you can buy.

I was content with 128 for a while, but after getting the Empeg, I realized that 128 wasn't enough. Getting the Empeg allowed me to listen in my car, which meant several things: a) The listening environment was more intimate, b) I tended to listen much much louder than at home, c) the amplification and speakers were better than at home. This allowed me to hear artifacts in the 128-encoded files that I hadn't noticed on the computer. These artifacts are usually in the high frequencies, and can be heard mostly on cymbals. Hi-hat and crash cymbals sometimes get swishy or crackly sounding at 128kbps. I'm now sold on VBR encoding at higher-than-128-equivalent quality settings to get rid of these artifacts. My only real choice now is between AudioCatalyst and LAME as my encoder.

Also, just out of curiosity, what do you people listen to to test out your systems?

I have an entire playlist of 40 songs on the Empeg devoted to nothing but test audio. They cover a range of frequencies, and I can listen for different characteristics in each one. Here are some highlights:

The Cape- Trevor Rabin
Subsitute For Love- Madonna
Ray of Light- Madonna
Vision of a Kiss- The B-52's
Follow Your Bliss- The B-52's
Red Rain- Peter Gabriel
Riot Proof- Tori Amos
Trip Like I Do- The Crystal Method
It Don't Hurt- Sheryl Crow
Papa Was a Rollin' Stone- Was (Not Was)
Modoc- Steve Morse
YYZ- Rush
La Villa Strangiato- Rush
Cut to the Chase- Rush
The Soul Cages- Sting
Copperline- James Taylor
Please- Nine Inch Nails

I'm sure Doug Burnside will chime in here with his favorite test audio tracks.

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Tony Fabris
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Tony Fabris