SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    66793, 66792, 66791, 66790, 66789, 67007, 
    66714, 66711, 66706, 66704, 66697, 
    66696, 66692, 66725, 66721, 66312, 
    66282, 66281, 66662, 66619, 66618, 
    66617, 66616, 66615, 66614, 66613, 
    66612, 66611, 66610, 66609, 66608, 
    66526, 66206, 66205, 66204, 66203, 
    66202, 66201, 66200, 66199
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00057

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where