I'm having trouble with user account activation emails being eaten by everyone's spam filters, so I'm attempting to find a quality guide on how to optimize my server to get them past these filters. I'm sure it's not an extremely complex job, so any information to guides or tips would be really helpful.
It would be best to use a 3rd party SMTP for this. However, if you're considering running your own, you need to properly understand and implement techniques such as SFP, DKIM and DSBL checking to counter spam, both incoming and outgoing. Only then can you make sure that mails sent by you are properly validated. I wrote a small article on effective spam filtering around a month back which I hope is helpful in your case.