Your broker would send you the trade info (you just need to make sure they keep it correct, they do make mistakes throughout the year, and those should be corrected right away). After that, well, I always founf that it's a good idea to use a professional to do your taxes, unless you have something really simple (or 1040EZ :)).
Like Monkish said, the brokers offer services where they provide you with Schedule D already filled in. The part about broker mistakes still applies there though, so it's not a bad idea to verify it. For example, per Etrade-provided Schedule D, I made more last year than I actually did, it's a good thing I caught two of their mistakes on time (two of my stocks went through name change, and they didn't reflect my cost prior to that, instead putting my cost as 0. Quite a profit, eh?).
As for the programs, if you still want to do it yourself (well, if you only have a 1040 and Schedule D, it's not a problem to do it yourself), I've seen tax preparers (good ones, not your H&R Block ones) use either Quickbooks for taxes plus everyday accounting, or Lacerte (both come from Intuit). From what I can tell, Lacerte is more of a program targeted exclusively to tax preparers, and they charge quite a lot, but Quickbooks should be fine.
The usuals, whatever I post is my opinion, yaddayaddayadda. I'm still learning this, so if you listen to me, well, good luck to you :)