Well now. Lets see. As far as True Runes go, definatly gotta be Bright Sheild/Black Sword runes. I loved the story behind them and how they truely set up the behavior of the True runes. These are the ones that really began to explain that no matter what, if you don't have a super strong will, the True Runes will shove their will upon you and they will manipulate the world to fit their own gain (In this respect, maybe Luc wasn't so crazy after all.) I love how Konami used two best friends to show the strength of the runes and their desire to do combat but I think it would have been a heck of a lot better if they would have used lovers or even family members. But who am I to judge greatness.
I like the rune that that village into vampires too. The Night Rune I think it was. That had a really intresting story. I wish they'd go more into it though. Maybe make a game revolving around Neclord and Sarah and someone from their village. It was pretty strong too when you used Sarah. SHould have had a slave/charm spell though.
OH! And the Dragon Sword you get in S2. The one that talks and said its an incarnation of one of the true runes. I loved that darn sword. Took any chance it could get to crack on Vicktor.
Hmm I think the True element runes from S3 were a bit overrated. To have all the power they said they did in the history of the runes, some of them seemed kinda sorry. Take the True Water Rune. TO have frozen that much space even with some of its power still sealed (fi I remember it was still sealed at that point or something like that.) Yet, it wasn't much more than a suped up version of the water rune. I was expecting the True element runes to have more unique abillities other than just one new spell. Good stories for all of them though, just a bit overpower to me.
As far as common runes go...hmmm lets see...I always spam the resurrect rune if there is one. And I love the Pale Gate rune. THe animations have always been great and the attacks we were usually uber. Oh, and the combination of the Spark Rune and a fast character in Suikoden 2 was always nice. Put that thing on Nanami and you pretty much smack everything before it knows your there.

In my game, that WAS her true rune dammit. XD .