For some reason I stopped getting email from my server. I decided to check my webmail and I see I haev 55,000 messages in my inbox from the whole year. Most are spam and returned email errors but I see many emails that I have gotten in my outlook before.

I was wondering if someone can explain to me how webmail works. I was also wondering if anyone knew why I stopped getting email all of a sudden. I have not made any changes except upgrade my linux server to the latest php.

maybe you reached the limit of your inbox ? Means you stop getting new messages
And since you mentioned ur using outlook ,
Maybe ( just maybe ) on tools-accounts , double click your email account , go to the advanced tab and see if you have checked :
Leave emails on server and you didnt specify any DELETE rule after than , if thats the case would cause your webmail to be full after this time and would probably left all copies of email you already downloaded the whole year !

This happened to me a while back. Did you happen to check to see if the reason you were not receiving any new emails was because I ran out of disk space. To stop this I set the settings for my main email account to :blackhole: so any emails sent to that address would just be deleted. You can also set it to :fail: and they will just be bounced back to the person who sent them to you. I would check your disk space to see if it is at its max. Maybe that is why you stopped receiving emails.