When I first started downloading, I felt uploading was the bigger problem, so I wouldn't seed at all after my download completed in order to avoid getting in trouble. After a few weeks I felt a bit more comfortable with downloading and uploading.
My dad got a few notices while downloading through dht or something in the Vuze client. I helped him out as soon as I heard. I think being in NY with a fast home connection means we're more likely to connect with bad peers. That fact plus the fact that my career path would be put in jeopardy if I were caught make me relatively careful.
At first I used smaller sites. Then I stopped liking smallish sites for reasons other than their security benefits. Now I tend to use newsgroups more. But I like bigger swarms and have used some insecure torrent sources. I'm a bit concerned about using Pretome because I know there are tons of US users and I could be an easy target.
With dvr and the fact that I'm downloading a lot fewer movies, so I feel I'm not putting myself at risk as often. Very soon I won't be downloading at all. Once I graduate I'll just reopen netflix.