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 (
    87742, 87741, 87656, 87644, 87643, 87642, 
    87641, 87640, 87639, 87638, 87637, 
    87636, 87635, 87634, 87633, 87632, 
    87631, 87630, 87629, 87628
  ) 
  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 0.00048

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
87628 1.69000000
87629 1.69000000
87630 1.69000000
87631 1.69000000
87632 1.69000000
87633 1.69000000
87634 1.69000000
87635 1.69000000
87636 1.69000000
87637 1.69000000
87638 1.69000000
87639 1.69000000
87640 1.69000000
87641 1.69000000
87642 1.69000000
87643 1.69000000
87644 1.69000000
87656 1.69000000
87741 1.69000000
87742 1.69000000