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 (
    88194, 88192, 88190, 88189, 88188, 88186, 
    88185, 88137, 88136, 88135, 88054, 
    88053, 88052, 88051, 88050, 87782, 
    87781, 87697, 87696, 87695, 87694, 
    87581, 88552, 88551, 88550, 88549, 
    88548, 88547, 88080, 87985, 88796, 
    88795, 88083, 87879, 87704, 87693, 
    87690, 87587, 87586, 87669
  ) 
  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 0.00109

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
87581 1.69000000
87586 1.69000000
87587 1.69000000
87669 1.69000000
87690 1.69000000
87693 1.69000000
87694 1.69000000
87695 1.69000000
87696 1.69000000
87697 1.69000000
87704 1.69000000
87781 1.69000000
87782 1.69000000
87879 1.69000000
87985 1.69000000
88050 1.69000000
88051 1.69000000
88052 1.69000000
88053 1.69000000
88054 1.69000000
88080 1.69000000
88083 1.69000000
88135 1.69000000
88136 1.69000000
88137 1.69000000
88185 1.69000000
88186 1.69000000
88188 1.69000000
88189 1.69000000
88190 1.69000000
88192 1.69000000
88194 1.69000000
88547 1.69000000
88548 1.69000000
88549 1.69000000
88550 1.69000000
88551 1.69000000
88552 1.69000000
88795 1.69000000
88796 1.69000000