I'm in the process of collating top tips and resources about this topic. I've compiled a list of useful links (see below), which I'm adding to continually, but if you have any advice based on experience it would be interesting to hear about it.
For myself, I'm not totally convinced that ebooks need covers (some Kindle publishers don't include it anyway). However, I tend to create them anyway, usually using a combination of Flickr, Word and Paint.net.
But I'm sure there must be better options, especially for arrtistically-challenged people such as myself!