Where can I find motherboards (or chipsets) which works with linux (DDR2 & DDR3). Can ubuntu use whole 4GB of memory?
I buy Intel stuff to get the best compatibility. They tend to cost a bit more with far more basic features. They also tend to use very very well supported components and aren't especially prone to failure. Thus you continue to often get, what you pay for. And using very common hardware tends to help a lot with compatibility. Granted, I haven't had a motherboard that I couldn't run Linux on.
As for how much memory it can use.. The 32bit version of Ubuntu can use exactly 4GB of memory. Which means you'll usually have notably less than that available for program memory, as that 4GB address space has to be shared with video memory and other memory in the machine.
The 64bit build of Ubuntu can support a great deal more memory, about 4PB - which is more than anything you'll be using before the next few decades are over.
The trade-off in using 64bit software on a machine with less than 4GB of memory is the same program compiled as a 64bit binary will take more memory to run than its 32bit version. But you still may want to roll with 64bit on less than 4GB, if you need to do very high-precision math quickly.
I'll add these 32 versus 64 bit considerations aren't inherent to Ubuntu, but rather the x86 architecture and thus any OS on it is subject to the same considerations - Windows, OSX, Linux, BSD, whatever..
Anything that isn't the following is likely to have components that are well-supported by Linux these days:
Beyond that you shouldn't have any issues except possibly with some wifi hardware and graphics cards.