I run a couple of message boards, and I'm also a frequent visitor at others, like Carolina Huddle. It's a tough line to walk, especially since most ad networks control the ad situation by default, not the site owner.
This takes quite a bit of effort, but I'll share what I did to try and create a more balanced ad experience at my forums.
For reference / a visual of what I describe to do below:
Domer Domain - Shows Subscribe options on the homepage and optimized ad locations
Fan Clubs - Early Access, so I don't have subscriptions set up yet, but another place to navigate if you need ad placement ideas.
1. Ask the Ad company to stop managing the ads, and request the required ad codes.
2. Create new advertisement using the ad codes from above. Place them in the appropriate slots using the admin panel.
3. Next step requires the Pages application. If you have Pages, you can use the Custom Blocks feature to create and insert the sidebar ads.
4. Remove any video player ads. If you want to leave it on since it's a high earner, make it guests only.
5. Ask the Ad company to add a close button to the Sticky Ad if you use one and there's no open to dismiss it.
6. Ask the Ad company to remove interstitial ads, if they're being used.
7. Create member groups for subscribers
8. Create an ad-free subscription (requires the Commerce application). Have members go into that subscribers group.
Make it more valuable with extra perks for subscribers like more space for profile pictures (gifs), uploads, messages, different color name, etc.
9. Disable ads for the subscribers member group.
10. Add a subscribe widget on pages it makes sense
I'm sure I missed some stuff, and looking back holy hell is it a lot of work, but that's what I did to improve the experience as best I could without completely killing revenue, while adding subscription options.