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 (
    125018, 125017, 125016, 125015, 125014, 
    125013, 125012, 125011, 125010, 125009, 
    125008, 125007, 125006, 125005, 125004, 
    125003, 125002, 125001, 125000, 124999, 
    124998, 124997, 124996
  ) 
  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 46 Using where

Result

product_id price
124996 1.69000000
124997 1.69000000
124998 1.69000000
124999 1.69000000
125000 1.69000000
125001 1.69000000
125002 1.69000000
125003 1.69000000
125004 1.69000000
125005 1.69000000
125006 1.69000000
125007 1.69000000
125008 1.69000000
125009 1.69000000
125010 1.69000000
125011 1.69000000
125012 1.69000000
125013 1.69000000
125014 1.69000000
125015 1.69000000
125016 1.69000000
125017 1.69000000
125018 1.69000000