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 (
    104248, 104288, 104287, 102289, 102288, 
    102287, 102286, 102285, 102284, 102283, 
    102282, 102278, 104481, 104480, 104479, 
    104478, 104477, 104476, 104475, 104474
  ) 
  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 0.00065

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
102278 1.69000000
102282 1.69000000
102283 1.69000000
102284 1.69000000
102285 1.69000000
102286 1.69000000
102287 1.69000000
102288 1.69000000
102289 1.69000000
104248 1.69000000
104287 1.69000000
104288 1.69000000
104474 1.69000000
104475 1.69000000
104476 1.69000000
104477 1.69000000
104478 1.69000000
104479 1.69000000
104480 1.69000000
104481 1.69000000