Obviously you would like to offer your ebay customers a variety of forms of payment to purchase their goods off you, the easiest, simplest and most used is paypal (please see my, do I need paypal link)
After accepting credit/debit cards (not through paypal) some customers and I would say for myself less than 4% wish to purchase through cheque.
If the item the customer is purchasing is expensive you will obviously wait for the cheque to clear before sending the goods. In the UK the time taken for a cheque to clear can vary and in many cases can be up to 5 working days, in the meantime the customers might get rather anxious and feel the cheque should clear a lot sooner, so please make sure you clearly state in the advert the time taken for a cheque to clear and make sure to email them when you receive the cheque (if it is a large amount) to keep them updated and email them on dispatch, some powersellers have been given negative feedback simply due to customer/seller confusion regarding the processing of cheques.
Fortunately less and less people are using cheques, which makes life for most powersellers a lot easier.
If the items are not very expensive some powersellers send off on receipt of a cheque after checking the ebay buyers feedback, if its high it is unlikely that their cheque would bounce for items such a small monetary values.
Make sure your adverts clearly state your policy on accepting cheques.