Every anime studio has a mountain of submitted projects that will be made when we have money. Most of these projects were submitted by staff members but some come from freelancers or even fans. Every director, every producer, every animator has pet projects that they want to have produced. When they get into a position of influence sometimes they still want to produce them and they get done. Some are refused even then. Some are so dated that they wouldn't be interesting to audiences.
80% of the projects that sit in the drawers of the file cabinets are extensions of existing shows (yet another URUSEI YATSURA episode/movie), rehashes of existing ideas (RANMA + OH! MY GODDESS type things), and same-old me-too formula stuff. When a show becomes popular a lot of people come up with ideas that are very similar to it and (luckily) most don't get made. They have a shelf life of about one week longer than the original show lasted. Most companies want to see totally original ideas.
Some people ask why the most ridiculous and annoying and derivative ideas (say, like, the GINREI OVAs for instance) will be immediately rejected if an outside source submits them yet they will be approved easily if one of the producers submits them. The producers have special market knowledge and can tell that it will sell like crazy and that it isn't really a ripoff me-too fan-service sort of thing, at least not to the trained eye. This is what they say to each other when they know that the rest of the staff (and the industry) is deriding them.
In order to produce a manga as animation a deal has to be cut with the original creator and this is usually some money up front and a percentage of the total sales of the product and perhaps all related merchandise. It's a common misconception that all original creators own the rights to their work. In many cases a publishing company will take all the rights and own a project before they will publish it. Take, for instance, ORANGE ROAD. Matsumoto Izumi came up with the original idea, wrote and drew the manga but Shueisha (Shonen Jump's publisher) owns the rights to it. They helped sponsor the animation projects that have been done as well. He gets a percentage of any money made from sales of ORANGE ROAD but does not own it. Thus when he wanted to do the ORANGE ROAD story in Comic ON Volume 1 and wanted to use a piece of music from the ORANGE ROAD TV series he had to pay to use it. (The fee was a small amount for each CD-ROM pressed.) If somebody wanted to do an English translation of the manga he could not OK it because the manga belongs to Shueisha. Sometimes people cast the sponsors in a bad light, making them out to be greedy demons from hell. Sometimes that is a correct assessment. It usually isn't though. The sponsor either offers to buy the rights to the idea or they are offered the rights by the creator. Nobody forces the creator to relinquish those rights. (Except maybe for the yakuza guys who always attend rights discussions and sit in the back of their room cracking their knuckles and picking their teeth with long knives.)
The really important thing about the system in Japan is that the sponsors know that they will make more money if they leave the staff they have financed alone. The director and animators and designers are hired because they are known to be trustworthy (or at least partially sane) and they will do their best work without interference from "above". Directors having wide latitude to do what they want is one of the reasons that anime is so exciting and interesting.

Yet another example of why I prefer to work in the anime industry: Last week, I was sitting in a hotel room in Manila watching the Cartoon Network and eating all the chocolate out of the minibar instead of writing this column like I should have been and I caught an episode of a show I'll refer to (somewhat mysteriously) as "JQ".
In the first pat of the episode,the bad guys see some guy taking pictures of their secret base so the chief says, "Take care of him and make it look like an accident." To me, this brings up images of untraceable poisons and accidents on roads in bad conditions and such - very stealty tactics. The bad guys warm up their hoverplatform things and come blowing out like mini-tornadoes swirling desert sand all over the place and chase the interloper as he drives off in his pickup and shoot at him with flamethrowers. They chase him around, using about a tanker-truck full of napalm and eventually run him off a cliff, then go down to the wreckage and use the flamethrowers again.
The next day the interloper's boss, a local rancher who just happens to be taking care of our heroes, goes out to see the wreckage and says, "Hmm... Maybe this isn't an accident." This is not because of the sand blown in swirling sand patterns or napalm residue (which is probably still burning) in a trail down five miles of road but because of his keen intuition. Somehow I don't think I would have been proud to have my name seen next to the word "director" in those credits. Unless it was "Guy who disagreed strongly with director about the flamethrower thing."