Lots are a good deal in several situations, and not such a good deal in others.
Lots are good if:
You want a high percentage of the items in the lot.
You are an active trader/seller and you will actually get rid of the extras.
You are after one or more hard to find items in the lot.
Lots aren't such a good deal if:
You only want a small percentage of the items in the lot, and don't actively sell or trade.
You are only after very common ponies in the lot.
You don't have a lot of space to store extras while you're trying sell them.
If you only want two ponies in a 41 item lot, and you don't have any use for the rest of the ponies in the lot, then find them seperately. You'll save A TON of money, and usually can choose nicer condition ponies(you usually don't get the best pics of each pony in lots). If, however, you are looking to build up trade/sale stock, or you will use several items in the lot, lots can be bargins.
Personally, I buy lots when I want to increase my trade stock, but I trade very rarely so the ponies generally hang around here for years. I occationally do trade, and when I do it's a big trade(often $200+ deals), so I do like to have a large selection of ponies for my trade partners to choose from. I will have to thin it out a bit soon since my closet is overflowing with ponies!