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 (
    98240, 98239, 98238, 98237, 98236, 98234, 
    98233, 98218, 97607, 98225, 98224, 
    98217, 98200, 98179, 98176, 98165, 
    98078, 97968, 97967, 97537
  ) 
  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 0.00071

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
97537 1.69000000
97607 1.69000000
97967 1.69000000
97968 1.69000000
98078 1.69000000
98165 1.69000000
98176 1.69000000
98179 1.69000000
98200 1.69000000
98217 1.69000000
98218 1.69000000
98224 1.69000000
98225 1.69000000
98233 1.69000000
98234 1.69000000
98236 1.69000000
98237 1.69000000
98238 1.69000000
98239 1.69000000
98240 1.69000000