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 (
    99381, 99279, 92940, 99916, 99866, 99806, 
    99805, 99804, 99790, 99789, 99753, 
    99751, 99439, 99434, 99429, 99278, 
    99257, 99219, 99372, 99360
  ) 
  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 0.00062

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
92940 1.69000000
99219 1.69000000
99257 1.69000000
99278 1.69000000
99279 1.69000000
99360 1.69000000
99372 1.69000000
99381 1.69000000
99429 1.69000000
99434 1.69000000
99439 1.69000000
99751 1.69000000
99753 1.69000000
99789 1.69000000
99790 1.69000000
99804 1.69000000
99805 1.69000000
99806 1.69000000
99866 1.69000000
99916 1.69000000