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 (
    69132, 69131, 69252, 69412, 69405, 69404, 
    68938, 68937, 68936, 68934, 68933, 
    68932, 68931, 68930, 68929, 68928, 
    68927, 68926, 68925, 68924, 68923, 
    68922, 68918, 68917, 68915, 68913, 
    68857, 68856, 68855, 68854, 68853, 
    68852, 68851, 68849, 68846, 68842, 
    68841, 68840, 68839, 69286
  ) 
  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 0.00102

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
68839 1.69000000
68840 1.69000000
68841 1.69000000
68842 1.69000000
68846 1.69000000
68849 1.69000000
68851 1.69000000
68852 1.69000000
68853 1.69000000
68854 1.69000000
68855 1.69000000
68856 1.69000000
68857 1.69000000
68913 1.69000000
68915 1.69000000
68917 1.69000000
68918 1.69000000
68922 1.69000000
68923 1.69000000
68924 1.69000000
68925 1.69000000
68926 1.69000000
68927 1.69000000
68928 1.69000000
68929 1.69000000
68930 1.69000000
68931 1.69000000
68932 1.69000000
68933 1.69000000
68934 1.69000000
68936 1.69000000
68937 1.69000000
68938 1.69000000
69131 1.69000000
69132 1.69000000
69252 1.69000000
69286 1.69000000
69404 1.69000000
69405 1.69000000
69412 1.69000000