Moore's and Ebay are where I go to look. I have the generic track from TRU (imaginarum brand?). My train table came from Target. We've built our own set over the years piece by piece.
Allaboardtrains.com has good sales from time to time, and free shipping if you buy more than $69.00.
Another idea is to check consignment sales for tables and accessories. They get snapped up quick though.
If you have a TJ Maxx, they sometimes have trains and other items at a deep discount, but it's pretty much hit or miss.
You can get battery operated engines that will work with the wooden track and cars.
I think my son's first set included Thomas, the milk car, the barrel car, a cabose and a figure 8 set. The more popular engines are Percy, Edward, Gordon, Henry, and James. They make engines with girl names too. My 2 year old daughter plays with Emily and Lady.