Well, having just upgraded the system in my WE4 I'll make some recommendations but keep in mind that a lot depends on two very important thngs: Your budget and your listening preferences.
If you're used to the factory Concert II system and just want to go to the first level with a basic upgrade I'd suggest you go to Best Buy or CC and pick out a CD receiver in the $150 - $200 price range that looks appealing to you and has internal amps that produre at least 20 watts RMS per channel. Panasonic, JVC, Sony, and Pioneer come to mind.
Replace the dash and door speakers with 3 1/2 and 5 1/4 inchers in the $50 - $80 range. Then replace the 4 x 10s in the trunk with a pair of two or three way 6 x 10s in the $100 range.
Regarding amps, if you want to start off on the economy side, just pick up a 2 channel amp of about 50 watts per channel to drive the rear 6 x 9s and let the new head unit drive the fronts directly. You will get respectfull sound this way especially if you install a pair of bass blocker capacitors (Best Buy or CC) in l ine with the dash speakers. You can pick up an amp in the $100 range.
As for the sub woofers you hear so much about, you may want one sooner or later but it depends upon just how much bass you really like. Many find that a good pair of 6 x 9s produce all the bass they want so they go without a sub woofer. If you decide to go with a sub, you can pick up a 10" sub in a sealed enclosure which will fit in the package tray of you GN for about $150. You'll then need another amp which puts out at least 120 watts RMS in the bridged mode which should set you back another $150 or so.
So, cost wise you can do a basic upgrade in the $500 range without a sub woofer. The sub should cost in the $300 range including the amp. Of cource, professional installation will up the cost a bit and if you want more power that will also up the ante. Hope this gives you some food for thought.