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 (
    96111, 89233, 96931, 96923, 96621, 92921, 
    96897, 96889, 96826, 95940, 95939, 
    95938, 95937, 95936, 95935, 95934, 
    95933, 95932, 95931, 95930
  ) 
  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 0.00093

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
89233 1.69000000
92921 1.69000000
95930 1.69000000
95931 1.69000000
95932 1.69000000
95933 1.69000000
95934 1.69000000
95935 1.69000000
95936 1.69000000
95937 1.69000000
95938 1.69000000
95939 1.69000000
95940 8.99000000
96111 1.69000000
96621 1.69000000
96826 1.69000000
96889 1.69000000
96897 1.69000000
96923 1.69000000
96931 1.69000000