I think Nemesis has the biggest plot hole, and it even has a name: Shinzon.
1. Shinzon was created twenty years before Nemesis to be a clone of Picard. Why? Why would the Romulans of twenty years before have known where Picard was going to end up in the future? He would have just been captain of the Stargazer at the time, just another average officer commanding an average ship.
2. For some reason the Romulans put Shinzon in command of their forces during the Dominion war, even though they seem to hate Shinzon's guts. Again, why?
3. Shinzon and the Remans somehow build this huge battleship in secret under the Romulan overseers' noses. While being slaves. How the fuck did they manage to pull that off?
4. Shinzon somehow finds a Soong-type android, and knows how to reprogram it even though it's been stated in the past that no one knows how to operate Data's systems except Dr. Soong.
5. Shinzon needs Picard's blood to survive. So what does he do? He breaks B4 up into five pieces (why?) and hides them all over a planet with hostile natives who almost kill Picard when he tries to retrieve B4. WTF?
6. As stated above, time's running out for Shinzon who desperately needs Picard's blood. So why does he make Picard wait 17 hours before showing himself? And why does he waste time mind-raping Deanna when he's dying and Picard's right there
7. Why doesn't Shinzon just tell Picard the truth about needing his blood? I'm sure Crusher could have found a way to give Shinzon what he needed without Picard having to sacrifice his life.
8. Why does Shinzon decide to attack Earth? He doesn't have anything against humans; it's the Romulans he hates.
9. And on that note, why does he let the Romulans who helped him kill the Senate boss him around? Why doesn't he just kill them too?
10. And the worst offender of all: Why doesn't Shinzon have hair?