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 (
    100888, 100887, 100886, 100885, 100884, 
    100883, 100882, 100881, 100880, 100878, 
    100844, 100843, 100809, 100780, 100646, 
    100483, 99747, 100808, 100367, 100779
  ) 
  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 0.00057

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
99747 1.69000000
100367 1.69000000
100483 1.69000000
100646 1.69000000
100779 1.69000000
100780 1.69000000
100808 1.69000000
100809 1.69000000
100843 1.69000000
100844 1.69000000
100878 1.69000000
100880 1.69000000
100881 1.69000000
100882 1.69000000
100883 1.69000000
100884 1.69000000
100885 1.69000000
100886 1.69000000
100887 1.69000000
100888 1.69000000