Something I have asked myself several times since re-launching RD where the best place to have advertising is, the one thing I have always done is place the ads in there own area so they aren't hidden with regular content to trick people into clicking. I have found that the best place to put them is on the right column and footer, this is because if the ad server is slow it will cause your site to stall while it waits for the ads, if they are in your footer or in the right column your website navigation has already loaded with the main body of the content, so it causes less disruption.
Ever notice how many companies sell AdSense ready websites where your entire site is nothing but advertisement after advertisement and they claim they will make you a nice bit of money, I have never purchased one of these nor do I desire to buy one for simple reason if they claim it can make you thousands why are they selling them for $20 to $40 when they could just open more sites and make thousands more, the reason for me is obvious, the sites have the potential to make thousands but only if you chose the correct domain, if you had something like thisisalongurlitishugeohwowthisislong.com then its unlikely anyone will randomly stumble upon it, now if you had a url which was similar to a popular sites except with different spelling or a different TLD such as gogle.com or google.net or gomummy.com then theres a higher chance of someone stumbling on your website and maybe clicking ads if they are relevant especially if one of the ads go to the actual site they wanted, but if I owned such domains I would simply place my own ads on the layout instead of buying a glorified template.
It still baffles me how so many website owners still tell visitors publicly to click there advertisements, companies haven't become as successful as they are at offering advertising opportunities without finding ways to stop unauthorised clicking, it still seems most webmasters (especially of smaller websites) think if they say 'hey click one ad a day' then they will make money and get away with it, for one telling people to click violates most (if not all) advertising companies terms of service but if the same people click 1 ad each day the advertisers going to pick the pattern up quickly and more than likely terminate your account, its better to look at your account and see in a month you have made $10 than for it to say several hundred then one day that your account has been banned and you get nothing, I mean a few dollars may seem like nothing but that's if you think here and now, yes it will barely (if at all) cover your websites overheads but websites rarely (if ever) gain in popularity at a straight line, in fact theres no set measure which can be used to explain it, some websites start getting popular fast while some are barely getting hits for months/years then suddenly bang they gain a lot of steam, the best description I have seen is that websites popularity increase logarithmically meaning its like a snow ball effect one user links a few friends to your website then each of those friends links more friends and they link more friends and it keeps going. Anyways the point of that little sidetrack from telling users to click ads when the alternative is you make little per month is simple, if you get banned from the company now then your losing a few dollars a month, what happens when your sites big and you want to make money from advertising, sure theres a lot of companies out there but they may not meet your needs (for example I chose bidvertiser because they pay through paypal while most others I saw used cheque.
The point is always look to the future, it may seem like a nice way to try and make cash now but if you get banned then the money you will lose from advertising will sting. I like the idea of advertisements since they can be a nice way of making revenue to pay for the website and (in theory) mean webmasters wont continually put up donate now buttons with every post, although some probably still will to try and get every last bit of money they can, I have donate buttons on Baby Seal Productions and Rampant Designs but they are placed on there own page because if someone wants to give me money, I wont stop them but I refuse to pressure anyone to donate money by saying something like 'Save this site', 'Keep this website open' and so on, mainly because I wanted to open the site, the work I do on them is because I enjoy it (same as the webmasters who run there relevant sites on the network) and thats why I continue to do it, yes money probably would make me do more but I am happy with the websites current progress .
Anyways to just summarise, my tips with ads on your website:
If there pay per click don't tell people to constantly click them at least once a day because it creates an obvious pattern, Don't tell them on the website with the ads to click the ads to support the site and finally ignore how little your making now and think how much you could be making over time.
This is where I would insert some joke telling you to click my ads but lets not risk violating any TOS just for my crappy sense of humor.
Also expect a new blog soon, this is my 13th blog and I am not superstitious, I just don't want to die.
Advertising is a big part of the Internet, it wasn't till just recently I actually started using advertising on my websites, mainly because I realised just how good advertising is after the ad which appeared on explosm for Baby Seal Productions which brought in a nice amount of hits, I have gone through several advertising companies since BSP launched starting with AdSense which was suspended because Google found suspicious activities but never stated what they were in there generic email, all I can think is it was related to hits dropping when the ad was removed from explosm or the fact the server the sites are hosted on were subjected to numerous attacks during spring break, the reason I went with AdSense was they offered bank transfers and to be honest there easier and it means you wont have to walk into your local bank with a check that has a huge Google logo on it. Anyways after that I tried various alternatives which I never felt fitted with the website mainly because unlike AdSense they paid by cheque only and the advertiser has to buy the ad on your website so unlike AdSense if no one has specifically bought an advertisement on your website you just have a blank space with a your ad here button.
There is several options for advertisements, some websites may even sell ad spots directly, this is something I would recommend as secondary advertising, I rarely see anyone buy such ads on smaller websites, they work great for larger websites and since you are paid directly you are cutting out the middle man, my tips for advertising would be simple:
for a small site:
AdSense or what I now use Bidvertiser, they seem like a good company and they pay through paypal, here's a link to there website:
Medium sites:
AdSense and Bidvertiser are still good choices, the advantage of bidvertiser is your websites popularity has an effect on how much you make from ad clicks, you could also sell your own ads or use a service such as adbrite where the ads that appear on your website are purchased directly.
Larger websites:
Again the earlier options are fine, in fact I have heard of websites that make $100,000+ a year just through AdSense but if your websites big enough you could probably make more through selling ads directly on your website especially when you consider the $100,000 would be after Googles cut which no one really knows how much they make since Google don't disclose it.
Things to avoid with advertising:
I visit alot of websites and notice the same common complaints, pop-ups and pop-unders in my opinion can be a hits killer, they are a nuisance and chances are the users closed them before the ads even loaded, websites can make great money from just text links and they can be layed out in a way where they don't interfere with the visitors experience.
Don't force users to click ads, for one it violates the TOS, some specifically state you can't have text like please visit our sponsors our support us above the ads will violate the TOS, also if one ip is noticed to click every ad on the site then they tend to notice. I have seen websites display AdSense ads on a download page and state you need too click them before downloading the file, this was smart since most users would believe they had to click the ad when in reality there was just a timer script preventing the download button appearing for 10 seconds.
Never click your own ads, this is a simple one, you log in to your publishing account on the advertising companies website they can place a cookie on your pc that identifies you and the site plus they can compare the ips with clicks.
Don't overload your website with ads, theres nothing worse than a website where every second link is an advertisement, it makes the websites hard to navigate and can appear off putting.
One last thing I would say is, don't design your website around ads, for one if the focus of it doesn't interest you then your less likely to keep it up to date or keep interest in it, plus as ads are targeted at the user based on keywords or categories so whatever the topic of your website there will be ads available for it, although with some ad networks such as AdSense which use keywords your websites name and content will have an effect on the ads, take Baby Seal Productions for example, it has nothing to do with Baby Seals but all the Google ads were related to seals.
. 
