b]Reliability[/b]
I don't think it's fair for a post to ever say "my kit is reliable, I just turned 1000miles on my turbo", especially chasing it down with a "knock on wood" reference. I would try and find the people with F/I who have similar driving habits and mileage to yours. They will give you a good idea of reliability with similar driving styles. I think a lot of people are coming up on the 6-12month mark with their kits.
Reliability is determined by a lot of factors, the biggest one being the motor itself. We all know what the motors will hold at this point. Our motor is not built from the factory to hold 300hp+, let alone 400-500hp. That being said, if you go over that amount, you're asking for problems at some point in the future. This is not always the case, but there have been a lot of people with issues.
Our motors can be built to be very strong. Most of the Supra internals drop right in and we know exactly what they can all hold. The motor can be made bulletproof for driving on the street or on the track without too much trouble.
Another one of the big factors in reliability is the transmissions. We all know what the trannies can hold at this point. If you have a 5-spd, it will probably break sometime in the future with f/i. There seems to be one exception to this rule, but otherwise that seems to be the norm. Several people have bought new trannies in anticipation of the stock failure. Several have had their cars towed to the shop to find out that some of the gears are missing teeth or that an entire gear was shredded completely.
The stock manual wasn't designed for much power, just like the engine, and it has a breaking point. An upgraded clutch will help to hold more power, but for how long no one is certain. The most common solution is to swap in something stronger, like the v160 or r154.
The auto transmissions can be built up to hold more power without a swap. In its stock form, the auto will not hold any significant amount of power before breaking. There have been lots of instances where the auto trannies have held 350-400rwhp+ daily. There are many solutions from several vendors out there, so if you have an auto do your homework.
There are several options out there for ~300hp crank. This is probably as safe/reliable as you can be. Any of the stage I kits, turbo or s/c, should be sufficient and will make a night and day difference in the performance of your car. If you have an auto, make sure you get a kit with a solution to shifting. If you think you might want more, you're dreams of ultra-reliability may have to change.
Management System
The ECU is probably the most important part of the kit IMO. The rest is just hardware than you can purchase or have fabricated on your own. The key to each tuner is the difference in the ECU. This was one of the biggest factors in determining which kit I purchased.
The piggyback ecu has its ups and downs. If you are running relatively low power and near stock parts, they may work out very well. They will retain all of your stock features such as cruise control and airbags, while allowing you to make changes to the timing and fuel system in the vehicle. They also run simulators to keep the CEL away and to make the stock ecu happy. They have their downfall when you want to go large!

There aren't any piggyback ecu's out there that will allow the same options as the standalones.
Standalones will give you more flexibility in your tuning configuration. I believe the Motec, and I'm positive the TEC3, have the ability to piggy back the stock ecu as well. I don't know about the Haltec, but I would guess it can do this too(?). Just like with the piggy back, you retain all of the cars functionality (airbags, cruise control, etc), but you have a lot more freedom in how you tune your car. A standalone will be able to control any size injectors you might choose, ignition system, timing, etc far beyond where a piggy back can.
I'm sure I'm biased, but I think the TEC3 is an excellent solution. I believe it has all of the same features as the Motec and Haltek, along with a built in ignition system. It has a relatively nice, and easy to use, laptop interface. It really is Total Engine Control! Everyone raves about the Motec and Haltek units as well, but I don't have any hands on experience with them. I would recommend you do some research to help decide which standalone you want to utilize in you car.
Misfiring/backfiring
I haven't heard of a case of this with any of the standalone units, but I don't think its because of the units themselves. I think that the stock ignition system is to blame for this problem. All of the standalone implementations have required an ignition system to go with them, except the tec3 which has an ignition system built in (I don't think the Motec and Haltek have them built in).
Without the beefy ignition systems that go hand in hand with the standalones, there would be backfiring as well. The piggyback ECU's don't generally have an ignition system that comes with them. Those who have swapped in the HKS or MSD systems have resolved the issue. I really don't think this is an issue in determining which kit to buy.
Rant
Yes... there's more. . .
If you want your car to be ultra reliable, then f/i may or may not be right for you. The car is made to be ultra reliable the way it is from the factory. It is not designed to be ultra reliable with anything on it changed. When you start adding power and changing parts, you are directly affecting the reliability of the car. No two ways about it.
If you drive you car like you stole it, then there are going to be reliability issues. . .with or without f/i. Read through the forums and you'll see that our cars go into limp mode at the blink of an eye. There have been several stock, near stock, and bolt on only cars that have broken due to hard, or spirited, driving. The IS is not designed to be a street racing monster from the factory, it is designed to be a Lexus. Your task is to turn it into a street racing monster that suits your needs, from 250-500rwhp+ and still have a Lexus.
Speed costs money. How fast do you want to go? Boost can be very addicting. At some point, you too will want just a little bit more. The hunger for boost is fed with cash. Make sure you know what you're getting into.
Don't forget about safety either. The cost of a turbo kit is just that, the cost of the turbo kit. You don't get nice things like gauges, brakes, wheels, suspensions, etc with that price. You can easily spend a few thousand on parts just to make your car safe. Your wheels and tires will probably spin everywhere you go if you don't change them. Most of the stage one kits should put your 0-60 in the 5 second range. This is mostly useless on the streets, but when you punch it, you better be able to stop before you catch the minivan full of kids ahead of you. I'm sure it's already happened to you without f/i.
Turbo kits for our vehicles are expensive. Ultra reliability is always desired, especially when you're spending a ton of money. There are relatively cheap to insanely expensive options for what you can do with the IS. But be prepared, there are lots of expenses built into the f/i adventure, even if nothing ever breaks. The price tags on the websites don't include the extras. You can spend more on that extras than on a stage I kit. F/I is not for the weak hearted or for the stingy.
I guess I'll wrap this up, since I'm sure you guys skipped to the end anyhow. An ultra-reliable F/I solution is certainly possible with some of the existing tuner's kits. An ultra-fast F/I solution is also available with some of the existing kits. If you want the best of both worlds, expect to spend some cash. Anything is possible and I'm sure all of the shops can do the work. If you're good with the IS, you can build your own kit and use whatever you like. No matter what though, speed and reliability both cost money. You can build whatever you want, its your dream.