It depends :) How long you're planning to travel and what kind of travel prefer?
Personally, I've travelled from Moscow to Irkutsk via trans-siberian (to the Baikal Lake) last summer. This place is defenitly worth to look, if you like tracking, hiking and such things. Also take a look at south Altai. It's not right on your way, but you'll find there the most breathtaking nature of the whole Russia (imho). If you're interesting in visiting russian Cities, then, I don't think, that I'll surprise you, - Saint-Petersburg and Moscow - is what you're looking.
Also, I would consider another kind of transport. Some of internal flights is about the same price as tickets on train (most of avia-companies has season sales). over 5 years ago