Depends what your really after. Have you completely written off the idea of a sub? There's not going to be a such this as "a best upgrade" it will all come down to personel taste. Below is what i would consider if i was spending the money myself.
$1000 dosen't get you all that much when you begin to add up everything like, wiring, instalation, and things like LOC's to run additional external amplifiers.
There's no real point in spending money to upgrade any of your
rear components. For the money your thinking of spending, what you would end up buying to replace them would not be of much better quality than what's already in place.
The biggest improvement your going to notice is the upgrade of your front stage. If your not going to add a sub, then i would reccomend spending your budget on the best front speakers you can afford, and a suitable amp.
$400 Front speakers
A bit of sound quality VS pure output here
Ryda Car Audio - Boston SR60 6" Component Speakers($398.85)
Ryda Car Audio - Soundstream TRC.6N Tarantula - 6.5" Component Speakers($398.85)
Both are equally great set's of speakers, just depends on what your aim is.
$400 Amp ( I reccomend using a 4 channel amp bridged to give the most power up front)
Shopping Secure - Car Audio Specialists - Option Audio OAC160 (I'm a big fan of these Option Audio 4 channels at the moment, 350 RMS x 2 when bridged , for this type of money is very good value)
Leaving $200 to cover the remaining such as wiring, instalation ect. (Also look at using some form of sound deadning treatment for your front doors, to get the most out of your upgrade. Which is obviously cutting it a bit short, unless your doing some of the work yourself. But if you could stretch your budget by say another $150 or so, then these component's would work well.
Disconecting your centre speaker can also improve the imaging up front aswell. (If you have one)