Anyone using Hydra as their main editor has probably quickly become annoyed at its inability to save window states for files. While this hint doesn't get around that nasty little annoyance, it does allow you to change the default size to something more of your liking.
You'll need the developer tools installed to do this. Do a Show Package Contents on Hydra itself (control-click on the application and select that option from the pop-up menu), then navigate to Contents -> Resources -> English.lproj, and double-click on TextDocument.nib, at which point a bunch of windows will fly open.
Grab the TextDocument.nib window, select the Instances tab, and double-click on Window. Resize and move the resulting window to wherever you like, then resize the large blue box it contains to the same shape and size. Quit Project Builder; it will ask you to save, and make sure you select Documents Format when you save. And you're done.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20030813083718757