First place I hit up for any motorcycle related purchase is
http://www.newenough.com. Their prices are usually very competetive, and their customer service is hands down among the best. They've been incredibly friendly when I've called in orders, and they ship quickly. They also have great deals on closeout items.
After them, it's the typical shit. Every now and then
http://www.kneedraggers.com and
http://www.compacc.com have good sales, and their selection is good for some window shopping as well.
After that, and if there's something I need right now, I'll stroll down to Cycle Gear and see what they have. Sometimes they're good on prices, sometimes they flat out suck. But if nothing else, I can try stuff on if it's gear related, or check out quality if it's a hard part item.
And recently, Amazon.com started listing motorcycle parts, accessories, and gear. I've got a Prime membership, so for certain items it's free 2 day shipping or $4 overnight shipping. Haven't had to make a motorcycle purchase lately, but I keep window shopping to see if there's something I can't pass up. Their selection seems pretty good so far. If I pick something up through them, I'll report on any problem if it's encountered, though I've yet to have any problems with Amazon over shipping or customer service.