I personally think SDI is over effective. It gives you a good chance of invulnerability to nukes. It is either way overpowered or not near expensive enough.
Federal Aid Commission is fairly useless for it's price. 50 million for an extra 1.5mil per aid slot is not effective in war, considering you would be much better off if you just had the 50mil in your warchest to begin with.
Foreign Air Force Base is one of the most useful ones up there. Air attacks are the second most destructive type of warfare, this greatly enhances it.
Hidden Nuclear Silo seems useful especially considering the SDI, and its relatively low price makes it one of the best war wonders to get.
Pentagon is fairly useless except for raiders, as ground attacks are not a big part of large nation warfare. No wars are conventional nowadays.
CIA seems useful, though the cost is extreme to say the least. 250 spies is expensive, effective, but expensive. Along with the cost of the wonder itself.
Anti-Air seems useful, though not entirely worth the price until you get way up in infra.
*Edit* Almost forgot the most talked over one. Manhattan project is overpriced considering what it is meant for. It will take well over a month for a nation not in the top 5% to get a Manhattan Project, and they do not seem effective at all unless you are looking to get beaten down from a very VERY high infra. Otherwise the 100mil would be better placed in a warchest.