I use a hosted exchange service. Email subfolders and the emails there-in sync over the air, along with Calendar and contacts. Android is currently missing the capability (as far as I know) to sync Tasks and Notes, which sux. The added advantage to hosted exchange is that multiple PCs will have the same outlook data... subfolders, sent items, calendar, notes, tasks, etc.
I think an IMAP email server will give you more capability (over POP) as far as subfolders are concerned, and you won't have to pay for hosted exchange, which runs about $7-9 per month.