Part of this is understanding where your email is stored and whether you want to keep it or not.
Many people want to keep their messages rather than delete them. If that's the case, you need to organize them more. With POP mail (the default for Comcast residential service), you can't keep thousands of messages on the server. You need to delete some by either deleting them immediately when you download them, deleting after a week, or going to the server sometimes and deleting them or putting them in folders.
You could also switch to the IMAP beta program which works better for accessing your mail from multiple devices and doesn't seem to need to look at every message's header.
At some point, POP mail clients (such as the built-in mail on the iPhone) seem to stumble over too many messages on the server. How many is "too many" is unclear.
