I like a little bit of heel with my skinny jeans if I'm not wearing boots or converse sneakers with them. I feel like the converse cut me off short, but they are fun, so it's pretty easy to get past that.
If you feel that flats aren't flattering with your jeans, try a low or mid heel shoe. My usual shoe choice with my skinnies are a pair of Born clogs with a high-ish heel (4 inches, but it's a platform so it doesn't feel that high) that are decorated with studs. I like the clogs because I can wear them with or without socks, so I can wear them during the winter. If you go with a heeled shoe, I would pick something substantial like that rather than a more delicate high heel. (And you definitely wouldn't need to go as high as my example in order to get the effect of an elongated leg.)
I couldn't find a pic of my shoes, but these are similar enough for show and tell. Just imagine them with a few more studs, and more of a biker vibe.
http://www.zappos.com/born-wen.....n-metallic
http://www.zappos.com/frye-aud.....ap_pdp_acc
I have no idea if they are trendy or fashionable. I just feel kind of tough when I wear them, and that's good enough for me.