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 (
    66793, 66792, 66791, 66790, 66789, 67007, 
    66714, 66711, 66706, 66704, 66697, 
    66696, 66692, 66725, 66721, 66312, 
    66282, 66281, 66662, 66619, 66618, 
    66617, 66616, 66615, 66614, 66613, 
    66612, 66611, 66610, 66609, 66608, 
    66526, 66206, 66205, 66204, 66203, 
    66202, 66201, 66200, 66199
  ) 
  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 0.00140

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
66199 1.69000000
66200 1.69000000
66201 1.69000000
66202 1.69000000
66203 1.69000000
66204 1.69000000
66205 1.69000000
66206 1.69000000
66281 1.69000000
66282 1.69000000
66312 1.69000000
66526 1.69000000
66608 1.69000000
66609 1.69000000
66610 1.69000000
66611 1.69000000
66612 1.69000000
66613 1.69000000
66614 1.69000000
66615 1.69000000
66616 1.69000000
66617 1.69000000
66618 1.69000000
66619 1.69000000
66662 1.69000000
66692 1.69000000
66696 1.69000000
66697 1.69000000
66704 1.69000000
66706 1.69000000
66711 1.69000000
66714 1.69000000
66721 1.69000000
66725 1.69000000
66789 1.69000000
66790 1.69000000
66791 1.69000000
66792 1.69000000
66793 1.69000000
67007 1.69000000