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 (
    88313, 88312, 88311, 88310, 88261, 88260, 
    88259, 89141, 88890, 88747, 88679, 
    88678, 88336, 88392, 88206, 88205, 
    88204, 88203, 88202, 88201
  ) 
  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 0.00063

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
88201 1.69000000
88202 1.69000000
88203 1.69000000
88204 1.69000000
88205 1.69000000
88206 1.69000000
88259 1.69000000
88260 1.69000000
88261 1.69000000
88310 1.69000000
88311 1.69000000
88312 1.69000000
88313 1.69000000
88336 1.69000000
88392 1.69000000
88678 1.69000000
88679 1.69000000
88747 1.69000000
88890 1.69000000
89141 1.69000000