Hey Mike,
I've had the luxury of hearing about every exhaust available (thanks to many car shows and the recent Rally) and I've installed several of them so I have a first-hand view on quality, design, etc. Unfortunately, my subjective view of the sound volume and quality will not necessarily match everyone elses opinion!
For your shopping and comparison criteria, sound, appearance (tip design, finish, etc.), and weight savings should all be considered. As for the generation of less heat - a Jet-hot coated exhaust will have less radiant under-hood heat than the same system non-coated. In terms of an exhaust system's effect on engine water temps.... I'll take the minority position to tell you that there's likely NO measureable water temp reduction with any exhaust. While it's true that some exhaust systems may have a slightly improved airflow in the engine bay - this will have little effect on engine run temps. (We have water-cooled engines with the radiators located in the FRONT of the vehicle so ambient engine bay temps DON'T have that much of an effect.) That said, ambient air temps in the engine bay CAN contribute to higher air inlet temps if/when the airbox and intake manifold become heat soaked. The GT's programming is very reactive to air inlet temps as we all are aware.
For what it's worth, here's some of my impressions & opinions;
Group 1 - The Muffler Replacement Pipes:
Accufab - Popular. Priced right. "X-design" promotes HP. Lightweight. No attractive tips - but many prefer this "bare" look. Sounds great. Some owners have spoken of slight drone in the 2000 area.
Heffner - Similar design to Accufab. Uses balancing pipe instead of X-design like Accufab. Has better, more robust, mounting flanges than Accufab (my opinion). Has nice, dual-wall tips. A little pricier than some others. A little deeper sound than the Accufab. Heffner also offers a Rear Bumper Delete version of the exhaust with the tips moved back about 5.25".
Ida - Another exhaust similar in design to Accufab & Heffner - perhaps more closely resembling the Accufab. Ida was one of the first to market. I've not installed one of these so I cannot comment on mounting/construction. Sound is most similar to the Accufab.
Stillen - The new kid on the block. Like the Accufab it is a "X-design". The quality looks very good. Comes with Jet-coat finish and reasonably priced (compared to others). Straight, no-tip design. I think the sound most closely resembles the Accufab. Stillen allegedly working on Rear Bumper Delete version of exhaust.
Group 2 - Modified Muffler Design
Borla (Offered through Ford Racing) - This was one of the first available mufflers for the GT and consequently was quite popular. It is a scaled down version of the stock muffler and using the same mounts with about 75% of the size and about 1/2 the weight. Very nice, large, Borla tips. The tips are removable. There are two advantages. 1) there are more alignment possibilities and; 2) if you go with a rear bumper delete down the road, you can keep this exhaust and just use new (shortened) tips. The major criticisms of this exhaust is that early adopters thought the sound was too mild for the $ spent and the other critique is that it still employs a heavy (~28lb?) muffler. However, this muffler in conjunction with some up-stream mods is arguably one of the leaders in the quality of sound dept.
Group 3 - Exhaust Header Systems
Ford Racing Rear Exit Headers - This is the system that I use throughout the last year (~3,000 miles). It is comprised of headers that wind back into a Borla collector muffler (muffler is over-statement) and then out through some very attractive Borla tips. The rpm lung at start-up will be missed by my neighbors - NOT! Idle after start-up is tame. Throttle blips can send people running. It is possible to drive the car somewhat quietly but you have to have a very soft foot. Gas pedal from 1/3 to 3/3 is VERY loud. However, the system will not drone at cruise speeds and could easily be driven long distances without fatigue. However, absolutely no room to add cats or mufflers. If you get busted for sound or emissions, you are SOL with this system.
Ford Racing Long Tube Headers - This system replaces your exhaust manifolds and cats. It uses the manifold/cat real estate to route a nice, quality made set of long tube headers. The exit point of this system is EXACTLY the same as where the CAT exit was - so you have the exact flange and mounting. It is intended to be used with the Borla muffler. In my opinion the sound of this system is amoung the best for quality. (The Borla sounds good in the first place, IMO, but just too quiet. The Boral muffler "wakes up" when you have no cats in front of it. This system also has the drawback of not being able to add cats to it. There's no room.
Stainless Works Headers - Another high-quality header system. Similar to the Ford Racing Rear Exit Headers but owners have managed to squeeze in a small CAT which helps both with emissions and a (very) modest amount of baffling. I believe that this system is slightly louder than the Ford Racing Rear Exit Headers (The Borla Collector Muffler is a hair better at muffling compared to the small cats in the Stainless Works version.) advantage is that there IS cats. However, all cats no created equal and no known data if these cats will pass smog (sniffer) check. Unique (angled) pipe exit through exhaust surround opening. Unique look - purposeful.
Group 4 - Related Exhaust Accessories
Ford Racing Cat Delete Pipes - These are 1-1 replacements for your cats and will noticeably increase the sound volume. More than just a straight pipe, these substitute pipes have a very small resonator.
Stillen CAT Replacement Resonators - Similar to the Ford Racing pipes above, these have much larger resonators and stillen claims much better sound quality (their objective) as a result.
My Preferences (for what it's worth):
I will be installing the Heffner (Rear Bumper Delete Version). I really like the deeper tone of the exhaust compared to Accufab/Ida. I am a tip guy and Heffner uses some very attractive (double wall) tips that look great and afford some protection of the black exhaust surround trim piece. Concerned that I will miss my Ford Racing set-up too much, I will likely also have a set of Stillen Resonators that I will occasionally use in place of the cats. If it is too loud and/or smog time comes, I can put the cats in. The swap back and forth is not too difficult.
Runner up:
I also believe that the Borla Muffler used in conjunction with the Stillen Resonators will be a very good choice. I am doing this set-up on two differnt cars in the coming weeks and I believe it will be a very nice set-up. The Borla also affords you to do the Rear Bumper Delete in the future without having to buy another exhaust system.
I hope I haven't made many mistakes in the info I provided. I may have - so others can chime in and correct me and I apologize in advance if any errors.