"[When] a thought without sensual desire arose in me, I thought of it much. [When] a thought without ill will arose in me, I thought of it much. [When] a thought without harming arose in me, I thought of it much."
My first thought was that everything is sense desire. When I feel sympathetic joy that my parents are traveling to Machu Picchu in the spring, the joy I feel is a sensual pleasure in my mind. Perhaps they mean non-mind sensual pleasures. Like I need to adjust my pillow my neck hurts. That's a sense desire thought. I say adjust yourself, don't stay uncomfortable.
In the end I know roughly what wholesome and unwholesome thoughts are. Some lead to ruin and come from a small place, are selfish. Others are more large minded, take in the family, the community, the cosmos. The suggestion is to just label thoughts, and usually the changes follow just noticing. Some thought and reflection might go into examining patters and whether thoughts are wholesome or not.
And then the paradigm of wholesome thoughts are contained in metta, compassion, sympathetic joy and equanimity.