The only country among the 3 that doesn't like visa runs is Malaysia – the other two seem to welcome "grey area" tourists: if I remember correctly, the Philippines even offer tourists visa extensions in-country for up to a year.

As lambshaanxy says, it works until it doesn't. If I were in your situation, I'd probably spend more time, every time, in Thailand and the Phils, and go less often to Malaysia. Thailand also has (or had, I haven't kept up) two-entry visas, which, with a visa run to a nearby country like Laos and extensions, allowed for half a year. That could make your schedule slightly less hectic.

The only country among the 3 that doesn't like visa runs is Malaysia – the other two seem to welcome "grey area" tourists: if I remember correctly, the Philippines even offer tourist visa extensions in-country for up to a year.

As lambshaanxy says, it works until it doesn't. If I were in your situation, I'd probably spend more time, every time, in Thailand and the Phils, and go less often to Malaysia. Thailand also has (or had, I haven't kept up) two-entry visas, which, with a visa run to a nearby country like Laos and extensions, allowed for half a year. That could make your schedule slightly less hectic.