1. Anti-Nepotism - The President may not appoint his spouse and relatives by consanguinity or affinity within the fourth civil degree as Members of the Constitutional Commission, as Ombudsman, or as Secretaries, Undersecretaries, chairmen or heads of Bureaus or offices, including government owned-or-controlled corporations. (Sec. 13 par. 2, Art VII, 1987 Constitution)

2. Appointments extended by an acting President - Appointments extended by an Acting President shall remain effective, unless revoked by the elected President within ninety days from his assumption or reassumption of office. (Sec. 14, Art VII, 1987 Constitution)

3. Midnight Appointments - Two months immediately before the next presidential elections and up to the end of his term, a President or Acting President shall not make appointments, except temporary appointments to executive positions when continued vacancies therein will prejudice public service or endanger public safety. (Sec. 15, Art VII, 1987 Constitution)

4. Ad Interim Appointments - The President shall have the power to make appointments during the recess of the Congress, whether voluntary or compulsory, but such appointments shall be effective only until after disapproval by the Commission on Appointments or until the next adjournment of the Congress. (Sec. 16 par. 2, Art VII, 1987 Constitution)
Other Limitations:

1. The presidential power of appointment may also be limited by Congress through its power to prescribe qualifications for public office.

2. The judiciary may annul an appointment made by the President if the appointee is not qualified or has not been validly confirmed. [Cruz, Philippine Political Law, p. 195 (1995 ed)]