So far, I think 5 people were mentioned that were involved in Trudy's murder.
I can't remember all of their names, but I'll try to explain them.

1. The man in the hospital - (A while ago, there was an episode in which Monk visited a man in a hospital. This man was in a hospital bed, and was hooked up to some machines that were keeping him alive and at a minimal level of pain. He claimed that all he did was create the bomb, and that he was hired by a man with six fingers on one hand)
2. The man that has 6 fingers on one hand - (He was killed by the Sheriff in Part One of Mr. Monk is on the Run - The Season 6 Finale)
3. The Sheriff
4. "Dale the Whale"
5. "The Judge"

What role did each of these characters play in Trudy's murder?
Part Two of the Season 6 finale kind of confused me about this.
Who hired whom? Who paid whom? Who framed whom? Who killed whom? Etc.
Could someone try to clear this up for me? Thanks.

I'll try to keep speculation out of it, but here goes.
In "Goes to Jail" Dale the Whale told Monk that Warwick Tennyson was "involved" in Trudy's death and that Trudy was the real target, not Monk.
In "Takes Manhattan" on his death bed Warwick Tennyson admits to being the one who built the bomb that killed Trudy and says he was paid for doing so by a six fingered man. (At the time the network episode guide identified the man as "Frank", but in the episode Tennyson just calls him a "freak.") Tennyson does not admit to planting or detonating the bomb, but it's also not explicitly stated that he did not.
In "On the Run 1" the six fingered Man is revealed to be Frank Nunn. Frank recognizes Monk and seemingly admits that he was the one who planted the bomb and killed Trudy and that he doesn't know why because he was just a hired gun. He never knows why.
In "On the Run 2" we learn that Dale the Whale through his intermediary the Sheriff hired Frank Nunn (who had been hiding out in South America since Trudy's death) to plant a bomb in Riverton and kill the governor. Frank thought he would be meeting whoever hired him in that sculpture garden to get his payoff, but instead he got killed by the Sheriff and Monk got framed.

As far as we know the Sheriff had nothing to do with Trudy's murder. He met Dale after he got sent to prison, which would have been years afters Trudy's death. The jury's still out on Dale the Whale though when it comes to Trudy's murder. He knew Warwick Tennyson built the bomb. He knew the six fingered guy was the triggerman. This is speculation now, but chances are if he's not "The Judge" (who we now know hired the six fingered man to kill Trudy) he knows who is. Since he made it his business to know all about Monk and Trudy he may simply have figured out who wanted her dead. I just don't think he's the guy. It's too easy.

Oh, thanks.
That pretty much cleared it up for me.

Thanks Teresa...it's now more clear for me ...

Thanks Teresa. That makes sense and cleard up for me many things.

the sheriff wasnt involved with the murder of trudy he was just involved with the attempted murder of the governer.