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 (
    9935, 9943, 9939, 9947, 9945, 9936, 9940, 
    9937, 9944, 9946, 9957, 9941
  ) 
  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 0.00100

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 product_id 3 12 Using index condition; Using where

Result

product_id price
9935 940.000000
9936 1800.000000
9937 2250.000000
9939 1400.000000
9940 1400.000000
9941 1500.000000
9943 1200.000000
9944 1450.000000
9945 4500.000000
9946 8000.000000
9947 2070.000000
9957 200.000000