What you see marked as junk depends on your own junk filter setup. If you're starting to see lots of good files marked as junk...try relaxing the filter a bit & mark the good files as 'not junk'. The filter 'learns' over time & it's not perfect
Junk Filter

I'd be wary of files smaller than 2000 KB. Always keep your AV updated & scan downloads before you open them! Make sure that you've got some good antispy/adware programs as well. These are free & pretty good
Spybot S & D

AVG Antispyware (formerly Ewido)

Ad-Aware SE Personal

Ad-Aware 2007 Free