While it's possible to connect to a remote repository with an SSH key using pageant, it is far from being an ideal solution. For one thing, pageant can only keep the key in a decrypted form, which can be a security issue for people who tend to leave the computer unattended for periods of time. What more, unlike with secure password managers, pageant does not have any form of "locked mode" or "auto lock/close after idle time", making pageant a very insecure way for managing secure keys.
Now, while all of these can be seen as flaws in pageant, it does beg the question of why pageant must be used at all. In the case of PuTTY, a session can have a key path set to it, in which case the key's password is requested dynamically during connection time. A similar enhancement for TortoisePLink could remove the need to open pageant, right click, add key, select path, enter password, use repository, close pageant, rinse and repeat, for every short access to a key-protected remote repository, and replace it with a simple "enter your master password" dialog.
Not sure about in which format the keys should be, but I imagine PuTTY format would be the simplest to use since TortoisePLink is essentially an extension of PLink.