Legitimate email messages end up in the junk box usually because they contain "trigger" words or other characteristics that have been associated with spam. If you're concerned about hitting the junk box because of the content of your messages, there are a few ways around this:
1) Don't put a lot of content in the message. Put the content on a web site or blog, and use the email to get people to click a link leading to the content. (You have to give a compelling reason for them to click, though.)
2) In the past, a popular way to get by the spam filters was to obfuscate the trigger words so that they wouldn't be picked up. For example, spelling the word "money" like "m0ney" with a zero. The spam filters have become more sophisticated, and obfuscation can actually work against you. I have had success with inserting a hyphen in certain words to get around this (e.g., "part-ner" instead of "partner" -- yes, the word "partner" seems to be a trigger word for whatever reason).
3) Use a spam score tool such as the one offered here. I haven't used that one in years since I had been using the built-in one in Aweber, so I don't know how up-to-date it is with its scoring. (I say "had been using" because I recently got rid of my Aweber account.)
4) You can also set up accounts at the major providers like Gmail, Hotmail, Yahoo, AOL, etc. and then send some messages to yourself to see if they get inboxed. If they show up in the spam folder, keep modifying the content of the messages until they show up in the inbox.
Another reason that legitimate emails can end up in the junk box is that they're being sent from a domain or IP address that has been blacklisted. This can happen to you if you're running autoresponder software (or just sending emails, period) in a shared hosting environment where someone has used the host's resources for spamming. This happened to me recently -- I was suddenly unable to send email from my hosting account because someone else on the same server started using it for spam. The host got the block lifted, but it was a major inconvenience.
Now it sounds like you don't want to use a subscription service like Aweber, so that leaves you with the option of running autoresponder software on your own server. This can work well, or it could fail miserably. The advantage of using a reputable third-party service is that they continually work to make sure that emails sent through their servers are whitelisted and inboxed.
Having said that, there is a decent program that you can host on your own server if you want to go that route. It's called AutoResponse Plus (not an affiliate link), and it's a pretty solid program. I used an older version of it about four years ago. I see that it's still around, and it's been updated, so that's a good sign.
Another option is Interspire Email Marketer (not an affiliate link). I haven't used it, but it's a fairly big name in the self-hosted autoresponder world.
If you want to go free/cheap to test things out with your list, you can try FeedmailPro (not an affiliate link). It's meant to be used in conjunction with a blog, but they have an API that you can use to add subscribers whether or not you have a blog. You can also import your lists from elsewhere without having to ask the subscribers to opt-in again.
There are other newsletter list management solutions out there, but I'm not familiar with them, so I don't want to make any more "recommendations".