They’ll always come with a warranty. Applecare is an extended warranty, which can be very nice to have if you have problems later on. That’s really up to you, though. My own policy is that I buy it for laptops but not for desktops. I can’t tell you what to do, though, you just have to decide if you want to risk your computer breaking or not. Rest assured, if you get it home and it’s broken that will be covered no matter what you do.
There are lots of places to buy new Macs:
Apple.com (and real stores)
powermax.com
Smalldog.com
bhphotovideo.com
macmall.com
compusa.com (and real stores)
That’s just a few, there are many others. Whatever you do, check the price of RAM at crucial.com first. If it’s less there, buy it put it in yourself. If one of these places offers it for the same amount, let them do it.
Some places will allow more custimization than others, although if you call them on the phone they’ll probably offer even more changed than their web pages admit. Some will have deals or sales running. If you find two sites have the same price but one is offering a free printer, well, take that into consideration.
If you’re looking to put together a real high-end system with extra video capture cards there are even places that will sell you systems already built for that. I can’t suggest any as I’ve always put what I need in them myself, but others here will know.