The Casino can only be built if Legalize Gambling ordinance is enacted, otherwise it won't be available. The side effect is that it acts as a huge magnet to crime, on top of the crime increase caused by the ordinance. While it does increase commercial desirability around it, the crime mostly negates the effect.
The Federal Prison should be kept away from residential areas as it has a tremendous effect on residential (as well as commercial) desirability. However, it does act as a larger jail in case you need the capacity.
The Missile Range easily provides the most income of all the business deals. However, there's a chance of a misfire, which can hit the city and destroy several buildings. This makes it a quite risky business deal to utilize.
Toxic Waste Dump
The Toxic Waste Dump generates huge amounts of pollution, including radiation, which means it cannot be built anywhere near civilization since Sims abhor radiation. It does provide quite some income, though.
The Army Base is another producer of radiation (even if not much). However it does have a slight positive effect on commercial desirability and, interestingly, increases the industrial manufacturing demand cap. It may be the most worthwhile out of all the business deals.
The Mayor's House acts as a large park in that it tremendously increases desirability for both residential and commercial population around it. It also has a slight positive effect on the Mayor Rating.
House of Worship 1
The cemetery's main purpose is removing air pollution. As it's free as well, there's no reason to not build it.
Even though this has a slight positive effect on its surroundings, the main reason for this reward is decoration.
House of Worship 2
Simply an another House of Worship, with the same effect.
Another Mayor's Statue to build in the city.
The State Fair doesn't have too many good things about it. It raises commercial desirability, but is a huge crime magnet, which pretty much negates the aforementioned effect.
The University is a great help to any educational system, however it is extremely expensive so you will not be likely to be able to afford one until late in the game.
Major Art Museum
The Major Art Museum provides a great boost to education especially for older Sims, however it is very expensive to maintain.
Another cemetery for you to build.
Minor League Stadium
The Main Library is the average people's counterpart to the Major Art Museum. It's cheaper and probably more worthwhile to get (but still rather expensive).
House of Worship 3
Another House of Worship to build.
Another Mayor's Statue to build.
Disease Research Center
The Disease Research Center cause a boost to health. Its capacity is very high; however it will most likely never get very many patients so the capacity cost is negligible. It also generates radiation.
The Opera House is not a good building to build. Not only is its maintenance cost rather high, but due to a bug, it will actually reduce education in large cities due to overcrowding.
The Television Studio is similar to the Radio Station in effect. However, do not build it in your residential areas as people do not like to live next to one.
Another cemetery to build.
The City Hall doesn't do much other than being decoration. It has a slight positive effect on commercial areas.
The Courthouse has largely a similar effect to the City Hall, and isn't much more worth it either.
Bureau of Bureaucracy
Same here. Especially the requirement of a fully funded health and education system, which creates extreme additional costs, makes this not at all worthwhile to pursue.
Major League Stadium
The Major League Stadium is basically a beefed up version of the minor league stadium. However, it is quite expensive. Like the minor league stadium, keep it away from residential areas.
The Movie Studio doesn't have much of an effect, but since it's free, there is no reason to not build it.
House of Worship 4
Another House of Worship to build.
The last statue of the player for the city.
As its name would suggest, the Stock Exchange is excellent for the commercial areas.