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 (
    5362, 5352, 5694, 5693, 5692, 5691, 5686, 
    5676, 5634, 5940, 26680, 6076, 6072, 
    6067, 6413, 6421, 6517, 6474, 6380, 
    6790
  ) 
  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 0.00088

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
5352 1.69000000
5362 1.69000000
5634 1.69000000
5676 1.69000000
5686 1.69000000
5691 1.69000000
5692 1.69000000
5693 1.69000000
5694 1.69000000
5940 1.69000000
6067 1.69000000
6072 1.69000000
6076 1.69000000
6380 1.69000000
6413 1.69000000
6421 1.69000000
6474 1.69000000
6517 1.69000000
6790 1.69000000
26680 1.69000000