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 (
    96513, 96512, 96511, 96510, 96503, 96384, 
    96086, 95838, 94773, 95878, 96342, 
    96341, 96340, 96343, 96337, 96336, 
    96335, 96322, 96313, 96182
  ) 
  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 0.00074

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
94773 1.69000000
95838 1.69000000
95878 1.69000000
96086 1.69000000
96182 1.69000000
96313 1.69000000
96322 1.69000000
96335 1.69000000
96336 1.69000000
96337 1.69000000
96340 1.69000000
96341 1.69000000
96342 1.69000000
96343 1.69000000
96384 1.69000000
96503 1.69000000
96510 1.69000000
96511 1.69000000
96512 1.69000000
96513 1.69000000