I'll second Kenwood as a good choice. Pioneer also makes a good stereo with lots of options for a low price. If you're going for something that's a little better, I'd go for Alpine, very clean, crisp sound from an Alpine.
If you're looking for ipod connectivity it's important to get a stereo that can actually control the ipod and not one that just has an auxilery input. The second important aspect is to get a screen that will show the information you want to see for your ipod lists, that means getting a decent oled screen. Oled is the kind of screen that doesn't look like a digital clock. It'll probably have some silly animation on it at the store but that screen will make ipod navigation much easier. I personally suggest Pioneer for the ipod interface alone, very easy to use, the main dial works very similarly to the ipod's actual controls.
Look for a unit that has at least two preamp outputs, three if you're thinking you might want to change this into a truck that will really get that windshield shaking. The issue with preamp outputs is how many amps you can hook up to the deck. One allows you to hook up one output, fine if all you'll ever want is a sub. Two allows you to hook up two amps, one for the sub and one for the regular speakers but you'll lose your fade (front - back) speaker control. Three preamps will allow you to hook up two or three amps, even with only two amps, the additional preamp will still be used so you'll have your fade control.
If you plan on adding an amp for a subwoofer but not for the regular speakers I'd also like to see high pass cross overs built into the deck, this will allow you to cut out the low range bass being sent to the regular speakers. Once the regular speakers are just doing the highs and mids you'll see a big difference in how accurate and loud they'll go. There's a big difference between just turning down the bass and actually removing the low frequency range. Trust me on this one.
On this same note, it's also good, albeit not completely necessary, to have sub woofer control on the deck, look for a low pass crossover (sometimes called low pass cutoff) and gain control (sometimes just called sub volume.) These are both available on any decent amp but it's nice to have the capability to tweak them without having to get out of the car and get out a tiny screwdriver and fiddle around in the trunk.
As for the regular speakers, I'd suggest seeing what kind of performance you get out of your factory ones before you buy something new. The additional power and cleaner signal that comes from any aftermarket deck may be enough to make you happy. It's also entirely possible to put together a good sounding stereo with a subwoofer but still keeping your factory speakers. Remember those high pass crossovers, here's where they really shine. Try turning on a high pass filter, there are usually three levels of cutting out progressively higher frequencies, I think you'll be very surprised how loud they'll go without distortion without the low bass frequencies.
All of that being said, sometimes the factory speakers just won't cut it. I'd suggest at minimum getting alpine or pioneer speakers (their car speakers are actually made in the same factory.) If you're looking for something a little better I am a huge fan of Polk Audio or Infinity but frankly, speakers are really a personal preference as to what sounds best to your ear. Here's a minimum of what to look for, polypropolene dome (plastic speaker surface) apposed to paper and rubber surrounds, apposed to foam.
For Subs, and I won't get into this too much, but for your average listener, either one ten inch or one twelve inch in a sealed box is plenty. The key is to get a decent brand, that's why one is plenty. The minimum I'd suggest is JL. I really like Alpine amps too, they're reasonably priced and they sound great.
