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 (
    103647, 103646, 103645, 103644, 103643, 
    103642, 103641, 103640, 103639, 103638, 
    105262, 105261, 105260, 105259, 105258, 
    105257, 105256, 105255, 105254, 105253
  ) 
  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 0.00073

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
103638 1.69000000
103639 1.69000000
103640 1.69000000
103641 1.69000000
103642 1.69000000
103643 1.69000000
103644 1.69000000
103645 1.69000000
103646 1.69000000
103647 1.69000000
105253 1.69000000
105254 1.69000000
105255 1.69000000
105256 1.69000000
105257 1.69000000
105258 1.69000000
105259 1.69000000
105260 1.69000000
105261 1.69000000
105262 8.99000000