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 (
    88722, 88721, 88720, 88719, 88718, 88717, 
    88716, 88715, 88714, 88713, 88712, 
    88711, 88710, 88709, 88708, 88707, 
    88706, 89080, 89079, 89078, 88676, 
    88675, 88674, 88920, 88919, 88493, 
    89075, 88916, 88491, 89082, 89030, 
    89029, 89028, 88996, 88995, 88994, 
    88993, 88981, 88520, 88495
  ) 
  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 0.00093

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
88491 1.69000000
88493 1.69000000
88495 1.69000000
88520 1.69000000
88674 1.69000000
88675 1.69000000
88676 1.69000000
88706 1.69000000
88707 1.69000000
88708 1.69000000
88709 1.69000000
88710 1.69000000
88711 1.69000000
88712 1.69000000
88713 1.69000000
88714 1.69000000
88715 1.69000000
88716 1.69000000
88717 1.69000000
88718 1.69000000
88719 1.69000000
88720 1.69000000
88721 1.69000000
88722 1.69000000
88916 1.69000000
88919 1.69000000
88920 1.69000000
88981 1.69000000
88993 1.69000000
88994 1.69000000
88995 1.69000000
88996 1.69000000
89028 1.69000000
89029 1.69000000
89030 1.69000000
89075 1.69000000
89078 1.69000000
89079 1.69000000
89080 1.69000000
89082 1.69000000