Is there difference between value of Scopus- or ISI-indexed paper in gaining acceptance for PhD?
At least in the US, PhD admissions committees do not care whether the journal an applicant has published in happens to be on one list or another (there are plenty of really low-quality journals in both of those lists, and high-quality journals not in them). Rather, they care whether the journal is reputable and highly regarded, and whether the paper itself is any good.

tl;dr Aim to publish solid, high-quality work in a journal that is known for publishing solid, high-quality work.