The main way I've made money in flash games is through sponsorships. It takes a while to get in contact with them all and on top of that even getting a reply sometimes can be difficult when first starting out. Luckily for me I was able to strike a good partnership with Armor Games and usually go with them the most. However they don't always want all my games so then I would seek out others, but I going to them first though shows loyalty and gives him first choice to improve success. Below is all the sponsors I have used. Theres many more out there though.
Networking is very important, try not to bother them until you've made something good to get on there radar. Half the battle is just being noticed, once you are in contact things get easier. So if you are just starting out don't worry too much if you don't get emails back, release the game with ads and just move onto your next game and try them again and try present the email in a quick easy to read way.
Overall my sponsorships have varied from as little as $100 all the way up to $5000. I've heard of big games making even more than this, but I havn't been able to break higher yet. I think if I totaled all my games sponsorships, I would have made around $30k - $50k. Also talk to sponsors about in game ads. You want to try combine as many revenues as possible for maximum profit.
By far the best sponsor I've worked with. The owner is called Dan and is friendly, offers good prices and is very understanding. Overall I've found him the best to work with above all else, he also responds to my emails quickly which I really appreciate. Games do need to be of good quality though, if you've made a great game check them out for sponsorship.
A pretty popular site, the owner is called John and is very easy to talk too. They are very strict on what they sponsor though and will only take really good games, however he always is willing to check out new stuff.
A very hard website to get hold of, and even harder to get sponsored. If you are lucky enough to be chosen though they have a collection of over 40 portals in all different languages. Which means you have to translate the game to all languages to be released with them. I've only ever done that once with Heaven and Hell and it was a tiring process but they did offer a good price to make it worth it.
This website I think has moved onto a new portal recently, so I'm not sure which branding they sponsor under now. They sometimes offer very low deals but can be negotiated higher which I often did. They were good for games I didn't get sponsored elsewhere as they are willing to take a higher chance on games.
Not sure if they are still sponsoring, but I had a few smaller games for lower amounts sponsored through them which was good and they were friendly and easy to work with.
Getting sponsored by Newgrounds is rare, they only take the best of the best and sometimes they don't even do that. They more lean towards putting there in game ads in, but if you think you've made a great game then give the owner TomFulp an email, he offers very high prices if the game is great. They also sometimes sponsor really good animations.
Kongregate started out sponsoring smaller games but I think they have now raised the bar. They usually offer performance deals which can be a mix of in game ads and there logos. The better the game does the more money you make. This is a risky move, but can be very profitable if you think the game will be viral