Motherboards can come in different sizes but the two most common ones are ATX and Micro ATX. Im not sure which one you have but a lot of companies use Micro ATX like my Advent had.
As for the Hard Drive connections, you can have either IDE or Serial ATA. There are others but these are the most populat ones and on most boards you get both types of connections.
Requirements for the CPU are normally listed on the motherboard specs page and will show a maximum of what speed it will allow.
If you are upgrading both CPU and Mobo, what CPU are you going to want, AMD or Pentium. If your gonna use your comp for gaming then i suggest a skt 939 AMD 64bit processor, if not then an Intel Pentium 4 is a good choice.
Take a look on Newegg or something like that and pick a nice package and I will do my best to advise you but since most of the best boards out there are ATX, I would advise you to change your case unless it does support ATX and you wish to not spend anymore money