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 (
    13878, 13877, 13876, 13875, 13874, 13873, 
    13872, 13870, 13869, 13829, 13862, 
    13858, 13850, 13849, 13848, 13847, 
    13846, 13845, 13844, 13843, 13842, 
    13841, 13840, 13839, 13838, 13837, 
    13836, 13835, 13834, 13833, 13832, 
    13831, 13830, 13827, 13826, 13825, 
    13824, 13823, 13822, 13821
  ) 
  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 0.00077

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 80 Using where

Result

product_id price
13821 1.69000000
13822 1.69000000
13823 1.69000000
13824 1.69000000
13825 1.69000000
13826 1.69000000
13827 1.69000000
13829 1.69000000
13830 1.69000000
13831 1.69000000
13832 1.69000000
13833 1.69000000
13834 1.69000000
13835 1.69000000
13836 1.69000000
13837 1.69000000
13838 1.69000000
13839 1.69000000
13840 1.69000000
13841 1.69000000
13842 1.69000000
13843 1.69000000
13844 1.69000000
13845 1.69000000
13846 1.69000000
13847 1.69000000
13848 1.69000000
13849 1.69000000
13850 1.69000000
13858 1.69000000
13862 1.69000000
13869 1.69000000
13870 1.69000000
13872 1.69000000
13873 1.69000000
13874 1.69000000
13875 1.69000000
13876 1.69000000
13877 1.69000000
13878 1.69000000