In general skyscrapers do not perform as well as a combination of banner ads and box ads. Specifically the normal skyscraper, 120x600, performs very poorly and is not recommended for use. A wide skyscraper does better but still often a good horizontal placement will outperform it.
The reason I believe is because skyscraper ads are simply harder to blend into your content due to their height. If your site were in a language that reads from top to bottom, rather than left to right, this might be different, but as it stands the skyscraper is one format that is simply easy for users to ignore.
If you are bent on using it, for instance if you have an existing design you do not want to change and it'll only fit a skyscraper, consider using a wide skyscraper, also consider matching the skyscraper background to whatever your content is. Finally consider putting it near a left or right menu.
My best advice for skycraper ads though is to use a CPM ad network to fill that spot and use your contextual ad network placements within your content.
You should of course do your own testing, it could be that for your site skyscrapers do perform well. However in my tests a 428x60 between two paragraphs of content vastly out performed a skyscraper ad to the right of that content.
One place skyscrapers can work is when the content on your page is not really paragraphs of content. Maybe it is a list, a directory, some sort of game, etc. You cannot use a box meshed with content there, or a banner meshed with content, so you might as well put a skyscraper to the left or right of what you do have.
Link units are offered by Adsense, but not yet YPN, and work a little differently than normal ads. They are merely a list of links, with no associated ad copy, that point to Google pages with ads. You do not get paid when they are clicked on, but rather when a subsequent ad is clicked on. Still, you can use one link unit in addition to your 3 ads and so you might as well add it.
My favorite location for such a unit is within or below your menu. Your menu is typically nothing but links and so is the link unit so it meshes well. Also if anywhere on your page is a related links or further reading section, putting a link unit just below that is good as well.
You can also try using the wider horizontal link units stretching across your content, or perhaps in your footer.
One thing I do not recommend is stacking a link unit on top of or below an ad unit, such as a 728x90 ad unit right above a 780x15 link unit. The reason is that the link unit doesn't really generate new clicks so much as steal clicks from the ad unit.