(#゚ロ゚#) Interesting question. Here are my top 3. (≧∀≦)
Personally I love it when they do 69, I need more 69 scenes in my yaoi. ლ(´ڡ`ლ) I also like when the uke is riding the seme, if the uke is more on the dominating side it's even hotter (灬º 艸º灬). And lastly I'm with you on the side banging, especially if they're having a hot (probably messy) make out session.
Well, I've probably sinned enough for today. (●'◡'●)ノ
I also like it when the uke rides the seme. My most favourite position is when the seme stands and holds the uke completly in the air ( the uke has no contact to the ground) and his own body weight drives you-know-what deeper in his ass everytime the uke moves!ლ(´ڡ`ლ) I think the it`s called Ekiben. Here you have an example: http://www.mangago.zone/read-manga/dark_avengers_dj_just_fucking_die/mf/c001/22/
Unfortunately I haven't found much yaoi with this position. ╥﹏╥
What is your favorite position(s) in yaoi? Example mine is either from behind or on the side with the leg over shoulder just love these ones