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 (
    106113, 106112, 106111, 106110, 106109, 
    106108, 106107, 106106, 106105, 106104, 
    106103, 106102, 106100, 106043, 106042, 
    106041, 106511, 106510, 106509, 106029
  ) 
  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
106029 1.69000000
106041 1.69000000
106042 1.69000000
106043 1.69000000
106100 1.69000000
106102 1.69000000
106103 1.69000000
106104 1.69000000
106105 1.69000000
106106 1.69000000
106107 1.69000000
106108 1.69000000
106109 1.69000000
106110 1.69000000
106111 1.69000000
106112 1.69000000
106113 1.69000000
106509 1.69000000
106510 1.69000000
106511 1.69000000