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 (
    98472, 98471, 98470, 98469, 98468, 98467, 
    98430, 98392, 98377, 97901, 97817, 
    97108, 92932, 92931, 98391, 98386, 
    92930, 98380, 98379, 98378
  ) 
  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
92930 1.69000000
92931 1.69000000
92932 1.69000000
97108 1.69000000
97817 1.69000000
97901 1.69000000
98377 1.69000000
98378 1.69000000
98379 1.69000000
98380 1.69000000
98386 1.69000000
98391 1.69000000
98392 1.69000000
98430 1.69000000
98467 1.69000000
98468 1.69000000
98469 1.69000000
98470 1.69000000
98471 1.69000000
98472 1.69000000