It really is all based on what you want to spend, and how much sound output you really want. If you have a civic for example, you can easily get 1 12" sub to sound almost as good as 2 10's, but if you have a larger car you might want to go with 2 12's instead.
Crutchfield is a great resource in learning what you need for what subs, how to wire them, etc.. Or you can go here, to read up on things.
http://www.crutchfieldadvisor.com
If you ask me, of course, JL audio subs are a nice match for any audio system. Most people describe JL speakers as having "Tighter" bass, and its usualy more precise then some other subs. I have had experience with Kicker, MTX, Pioneer, and JL subs, and I rate my JL's above any of what I heard from the latter.
As for amps, I have had wonderful luck with Precision Power, Orion, and the older Rockford Fosgate amps *bat wing*. But all of these brands are a little on the pricey side.
If you want a simple system that doesn't break the bank I would suggest something like the Infinity Reference series line, or the Kicker Comps, perhaps a dual 10" set with a nicer amp to boot. Your amp will be the key for any speaker line-up. If the amp has the extra power, you won't regret it.
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Watts: Power
Remember to choose an amp that supplies power to the upper range of the speakers RMS power, this is the power it needs constantly to sustain propper performance. IE: If you get a pair or 50-300 watt RMS subs, that means each sub wants at least 50 and not more than 300 watts to operate. To keep the subs from distorting somewhat, try to select an amp that will provide at least 500 watts of RMS power, that will divide 250 watts to each sub, which should be plenty of output without risking any dammage. It would also be a good idea to buy something 600 watts, and leave your gain down just a tad in order to keep the amp from working itself to death and in some cases overheating.
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Ohms: Resistance
Look at your ohm rating and voice coils as well. If you purchase 2 single voice coil subs, that run at 4ohms, you can wire them standard *positive to positive, negative to negative* and your amp will see a 2ohm load *which is good* but only as long as your amp is "2 ohm stable."
http://www.crutchfieldadvisor.com/le...impedance=SVC4
If you decide to get a set of Dual Voice Coil subs that run at 4 ohms, you will need to wire them as seen in option 2 of the link below, which will result in a 4ohm load to the amp. This will cut down the power supplied to your subs. IE: if you have a 500 watt amp, and you are running at 2ohms, you get 250x250, if you are running a 500 watt amp at a 4ohm load, you get less power per speaker, probably more like 125x125 RMS, which means you would need to buy an amp that is 1000 watts, to supply that 250 per speaker.
http://www.crutchfieldadvisor.com/le...pedance=DVC4x2
Ohms are a fishey factor, but one to be educated about, because you can easily wire up a system thats not even working to half its full advantage, likewise you can easily fry an amp by running an ohm load that it will not support, like the 1 ohm setups that some of these diagrams list.
DO NOT wire a system to 1 ohm unless you have an amp that is "Stable" at 1 ohm.
I would suggest buying
single voice coil 4ohm subs, or
dual voice coil 2ohm subs, because both can be wired easily to a 2ohm load, which means you will be getting all the power the amp has to give.
If you need any help post again and we will figure it out, I know several decent resources for car audio, I have been reading up quite a bit, I am thinking about getting a competition stereo in the future for another vehicle.
Advice on amp/sub
