I'm not very familiar with all these federally funded programs in America, so I only searched a few on the internet. It might not be that comprehensive or accurate.
  I don't think any of the federally funded program should be eliminated. It's just the problem of whether the government has put the appropriate amount of resources to that sector or not. 
  One of the organizations that should be reduced is FBI. It deals with the issues of homeland security and safety. There is some overlapping areas that CIA also deals with. Even though these two agencies belong to different departments, they both need high intelligence, high technology and covering work. The cost on their agents' training and equipments should be rather high. I'm thinking maybe they could share some of the resources. They two have separate jobs and focus on different issues, so two are important. If they can really share resources, one could cut some of its funding or resources. 
  The other program that I think should be enhanced would be the U.S. Equal Employment Opportunity Commission (EEOC). They work to eliminate the discrimination such as race, sex and age on job application. As far as I know, there are still a lot of people not being treated equally. Women are not getting the same pay as men do, even though their workload is the same or even harder. Under such economic environment, the number of job applicants exceed the need of the market. Employers get more choices and they would prefer those younger people who can be more efficient on working. The discrimination can occur everywhere from job application process to the working environment. Therefore, I think this program should be maintained and enhanced.