There are two types of earmarks - those found in the statutory text itself ("hard" earmarks) and those found in the committee reports accompanying the bills ("soft" earmarks). Hard earmarks are, because they are in statute, binding law. Soft earmarks are not found in law (hence my description as "extra-legal"), and therefore may be ignored by the Executive branch when it carries out the law (more on that below). Only by passing a law, either with the President's signature or over his veto, may Congress bind the Executive branch; that is the sole avenue for them to act under the constitution - passing legislation.

That said, the Executive agencies who ignore soft earmarks in the reports do so at their peril. Those agencies who do ignore them may find themselves with more hard earmarks, or reduced funding, or other nasty surprises in the following fiscal year. The appropriations committees don't brook a lot of nonsense from the agencies when it comes to their pet projects. As such, most agencies have a good understanding with their appropriations subcommittee(s) about how soft earmarks will be treated.

The Executive may also tweak the soft earmarks somewhat in carrying them out, depending on the particular agency's other statutory authorities and requirements. For example, my own BGA has statutory requirements for cost-sharing when we do R&D or other work with outside entities, as well as regulatory requirements for application for aid, etc. By strictly adhering to the cost-sharing statute and application requirement (not that we'd do otherwise), some of the soft earmarks disappear because the intended recipients don't want to go through the process of applying for the aid and then proving that they are living up to the cost sharing requirements prior to the BGA's release of funds.