The app store probably wont be up until next year, when 10.7 comes out.
No, this is incorrect. As noted by Steve when he introduced them -- the Mac App Store will be up "within 90 days" (said at the end of October) and Lion will be out "next summer" (likely August).
One of my favourite sites to check for new and updated Mac software is MacUpdate.com, but there are plenty of others.
Finally, no there are no "preferred" sites -- and "safe" isn't an issue from any legal downloading site, because Macs don't get viruses. It is possible to pick up a "Trojan Horse" malware from pirated software, however, so my recommendation is that you stick to buying legal software, which supports Mac developers we could always use more of.
On top of that, most Mac software is SUPER cheap for the quality I find.