Outside of the graphic nature, and using my own limited observations, what I've noticed is this:
1. Yuri stories tend to feature girls who both act like girls. One might be more aggressive, or submissive, but it's rare for me to read a yuri story and think "one of these could easily be a dude".
2. On the other hand yaoi stories almost always feel like that to me (but in reverse). The emphasis on uke/seme relationship pairings makes one clearly "male" and the other feel very "female". The character designs don't help either, since all of the characters border on bishie overdose. It isn't uncommon for me to read a yaoi story where the submissive character is rather feminine in looks and personality...even drawn smaller than the aggressive character.
3. I agree with the others, that yuri subtext is really common even if actual yuri stories aren't. I think there's a general level of acceptance, where people have become more comfortable with yuri but not with yaoi, which I think is still somewhat more taboo than yuri. On the other hand....
4. .....going back to 1 and 2, many yaoi stories I have read feel almost heterosexual. I've read/seen many yuri stories that explore the complications and possibilities of the topic, but compartively fewer yaoi stories that aren't just about a seme dominating a uke and getting it on. That doesn't mean they don't exist, and those that do are generally pretty good, but many yaoi simply feel like a Josei story in different packaging.
5. Interestingly enough, this even branches into Hentai. Yuri stories are more explicit (obviously) but the themes generally remain the same (both leads are typically feminine). Yaoi stories are heavily themed in the sense of the uke being feminine, often to the point of crossdressing/genderbending. Futanari stories tend to go either way (pun intended?
). While Hentai is generally warped (as most hardcore pornography tends to be), it is interesting to see what authors will do when they aren't as limited by censors.