Misc. Mods
Brakes
The stock LS1 front brakes, when pushed hard, will warp the rotors very easily. The primary culprit here are actually the pads. GM chose a pad that created very little brake dust, but created a lot of heat that soaked into the rotors. The stock rotors can only take so much heat before they warp under the stress.
Brembo makes an inexpensive OEM replacement rotor that better stands up to heat soak. I also opted for a pair of aftermarket brake pads as well, in this case the PBR metalmaster pads. These pads do create more dust than stock pads (better clean the front wheels on at least a weekly basis or they're going to look like crap), but they are more rotor friendly and have better bite.

Lou's short shifter
Cheap and easy mod to replace the stock shift handle. This does not replace the entire shifter assembly like the Hurst or Pro 5.0 units. It is also not nearly as expensive as these units, and can be used in conjunction with these units if you so wish.
This handle is about 1.5 inches shorter than the stock handle, and it eliminates the rubber isolator that is in the stock handle. You end up with a shorter throw, and firmer feeling shift, but also get a bit more vibration through the shifter as well. What vibrations I've experienced have been very minor (and I've felt worse vibrations on stock shifts for other vehicles before). Overall this mod was well worth it, and I feel less like I'm shifting a truck and more like a pony car.

Kenwood CD player
MP3 is a great format. Nothing beats packing high quality music into a tenth of the space. I replaced the stock head unit with an MP3 compatible Kenwood CD player. I can fit 8-10 CDs worth of music onto a single CD and basically get all my current stuff onto a total of 4 disks (which gives me roughly 40 hours of music). It's not the greatest CD player in the world, and I lose my steering wheel controls, but it's worth the added flexibility. I would not enjoy going back to a regular CD player at all.
I also have a bazooka sub amp (600watts peak, 300watts RMS) and 2 10" subs waiting for install. These were originally installed in my previous 88 GTA (This is my 4th F-body). I have to get a new enclosure for the new TA though and run the wiring for the amp. Gonna wait till spring to mess with that.