there's a couple reg fix files available to reset the window placement. Just google "ie window placement".
There's one here close to the bottom under "IE tips"
http://windowsxp.mvps.org/

I haven't tried it myself but here's what the fix contains
REGEDIT4

[HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main]
"Window_Placement"=-


If you're going to try it, I would set a restore point first

 

Try this. Open a link. The window opens up small, right? Don't maximize the window, instead use the mouse to "grab" the edges of the window and drag it to a bigger size. You can drag it to almost maximized size. If you actually maximize it, this won't work.

Now, after you have it dragged to the new, bigger size, hold down the "shift" key and minimize the window while holding the shift key down. Now release the shift key, click the icon for the window that is in the task bar to open it, or rather "restore" it.

Now close the window, and the next time you open a link, it should open to the size you set the window to with this procedure.