To be truly sure you're back to normal, you would want to re-flash firmwares, as well. Which is truly a pain. Your NIC has firmware, your Motherboard has firmware, even SATA disks have firmware...
Here's a gentleman who put malicious firmware on a hard disk to bypass linux security by serving a neutered /etc/passwd file.
http://spritesmods.com/?art=hddhack
Generally, you have to choose the level of rebuild that you can live with given your likely attacker. Usually, flashing firmware is dangerous and likely to alert the operator to the infection, so most attackers interested in spam/phishing wouldn't try that approach. That is probably some three-letter-organization level stuff.