SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    88704, 88703, 88702, 88701, 88700, 88699, 
    88698, 88696, 88695, 88694, 88692, 
    88691, 88690, 88688, 88687, 88686, 
    88685, 88684, 89281, 102419
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00059

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 40 Using where

Result

product_id price
88684 1.69000000
88685 1.69000000
88686 1.69000000
88687 1.69000000
88688 1.69000000
88690 1.69000000
88691 1.69000000
88692 1.69000000
88694 1.69000000
88695 1.69000000
88696 1.69000000
88698 1.69000000
88699 1.69000000
88700 1.69000000
88701 1.69000000
88702 1.69000000
88703 1.69000000
88704 1.69000000
89281 1.69000000
102419 1.69000000