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 (
    89607, 89606, 89605, 89604, 89603, 89602, 
    89601, 89600, 90393, 90163, 90070, 
    90069, 90068, 89588, 89587, 89535, 
    89534, 90287, 89533, 90328, 90327, 
    89543, 89530, 89529, 89528, 89517, 
    89487, 89486, 90303, 90302, 90301, 
    90300, 90299, 90298, 90297, 90296, 
    90295, 90294, 90293, 90292
  ) 
  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 0.00086

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
89486 1.69000000
89487 1.69000000
89517 1.69000000
89528 1.69000000
89529 1.69000000
89530 1.69000000
89533 1.69000000
89534 1.69000000
89535 1.69000000
89543 1.69000000
89587 1.69000000
89588 1.69000000
89600 1.69000000
89601 1.69000000
89602 1.69000000
89603 1.69000000
89604 1.69000000
89605 1.69000000
89606 1.69000000
89607 1.69000000
90068 1.69000000
90069 1.69000000
90070 1.69000000
90163 1.69000000
90287 1.69000000
90292 1.69000000
90293 1.69000000
90294 1.69000000
90295 1.69000000
90296 1.69000000
90297 1.69000000
90298 1.69000000
90299 1.69000000
90300 1.69000000
90301 1.69000000
90302 1.69000000
90303 1.69000000
90327 1.69000000
90328 1.69000000
90393 1.69000000