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 (
    99241, 99240, 99239, 99238, 99237, 99236, 
    99235, 99234, 99233, 99232, 99231, 
    99230, 99229, 99228, 99227, 99226, 
    99225, 99224, 98584, 98573
  ) 
  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 0.00061

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
98573 1.69000000
98584 1.69000000
99224 1.69000000
99225 1.69000000
99226 1.69000000
99227 1.69000000
99228 1.69000000
99229 1.69000000
99230 1.69000000
99231 1.69000000
99232 1.69000000
99233 1.69000000
99234 1.69000000
99235 1.69000000
99236 1.69000000
99237 1.69000000
99238 1.69000000
99239 1.69000000
99240 1.69000000
99241 1.69000000