Dockable windows:
Seriously the current GUI is wasting space by showing the desktop and it’s showing 5 tabs instead of one tab (see below). 
Combining installations:
Seriously there should be one installation file not four.
In a sane window manager this wouldn’t be a problem (in GNOME on Linux I get one tab item for the toolbox and one for each image). I imagine this is a problem in the Windows version of GTK+ or in Windows itself rather than in synfig, you might want to ask the GTK+ folks: mail.gnome.org/mailman/listinfo/gtk-list
In an OS with sane package management (dependencies, repositories, etc) the multiple install files wouldn’t be a problem (in Debian I just do apt-get install synfigstudio). You might want to ask Microsoft to fix this, until they do, pixelgeek plans to make a workaround. Unfortunately he didn’t have time to do it before the 0.61.09 release.
If you would like to do some work on either problem, we would gladly accept your work.
Please add them to the wishlist page or features tracker if they aren’t there yet so we don’t forget them.
I would also bow for a one-window program. It’s just extremely annoying that everytime I want to open the program from the taskbar I have to click on four different tabs. Also, everytime I begin working on something again I have to resize every damn window to make everything cover most of the background so I won’t easily click between the Synfig windows. Also I don’t really see the positive side of four different windows.
I believe this is a GTK thing. Gimp has the same problem.
Chris
PS - I am working on the combined install. Hoping to make some progress on it the week after next.
HAHA! FINALLY i’ve found someone other than me that has noticed this problem! yes, it is quite a drag that synfig opens in 5 separate windows, instead of the usual one!
not for me, Gimp doesn’t! i have Vista, for the record!
i’m glad ur working on it!
YES! i totally agree! i addressed that problem on synfig chat room just recently, but got no real solutions! i hope someone comes up with a fix or workaround soon! 
Posting about the issue will not get it fixed. It is a well known issue. Only doing something about it will get it fixed. If you cannot work on the code yourself, please be patient and wait for those who can to do it. If you would like to wait less time, paying someone to work on it might motivate them to do it.