Thanks to reading lots of articles on HN about password security, I upgraded my site's passwords from salted MD4 to bcrypt about a year and a half ago (a bit late to the party, but still). Here's what I did:

I added a second password column to the users table, then ran a script that queried the table for the existing hash, generated a bcrypt hash from that value and wrote it into the new password column. Then I removed the old password column. No need to wait for the user to log in.

When people log in today, the code takes their password, runs it through the old hash routine, runs the output through the new hash routine, and compares that to the password on file.