"Why can't ANYONE in Trek marry their own species??"

Keiko and Miles O'brien? :p

bajoran surrogation in pregnancy
Miles possessed during wedding week

and even then they are marrying cross culture (Japanese/Irish and ops/ Sci)

it seems normal relationships
(1 man 1 woman same species and background) are unheard of

Chakote find the Rubber People ...

Oh boy, I've got a few of these.

"The Changing Face of Evil":
The Breen come along with their God-mode weapon, use it to destroy an entire fleet, and whilst they're all floating around helplessy in escape pods the Female Changling decides to let them all live. Because it'll be demoralising. Dead officers are less use than demoralised ones, and it only takes one person to deliver the message that they're all screwed anyway. I appreciate the series heroes cannot die, so why put them in a situation that they can only escape from because the series baddie is an idiot?

Any engagement between the Enterprise-D and Klingon Birds of Prey:
"Rascals" - two surplus Birds of Prey (how often do you think the Klingons scrap non-obselescent warships? Never?) defeat the Enterprise because Riker fires one shot back at them. Even with ample time to warn them, I still think the Enterprise should've won that engagement, hands-down. You also never see more than about eight Ferengi who are able to subdue a huge ship with over a thousand people on it, without the aid of the main computer, by the way. Crew lockdown or not, that's a stretch.
"Generations" - again, Riker only orders one shot fired, and then spends time looking for a way to disable them, instead of just unleashing the HUGE arsenal he has under his command at it. Would've been a lot quicker, imo.
"Yesterday's Enterprise" - this one's less annoying, since there are three BoPs and they're presumably frontline. But the Enterprise still seems to spend a lot of time not shooting at them. And they destroy one with a torpedo spread and about three phaser blasts.

When you compare those battles with the amount of ordinance the Enterprise fired at the Borg and the illusory Husnock ship, you have to wonder why the Enterprise couldn't just blow the BoPs out of the sky completely in a few seconds.

"A Night in Sickbay"
A dog pissing on a tree and Archer not getting any nookie is a suitable plot of a Star Trek episode now?

"Threshold"
I don't need to explain this, do I?

"Star Trek V"
There's a lot of stupid in this, but I think I'll settle for the plot hole that basically sets the whole movie off:

Kirk: "Why send us, this ship isn't ready! Half of it isn't working! We don't have a full crew etc."
Bob: "I need Jim Kirk out there."

So send him on a functional starship. Or send him as a mission specialist with someone else. And do you know what? He does nothing to justify his supposed necessity to the mission. All he does is make a sneak attack which basically fails.

The problem with Voyager is that they put a relatively small ship out there by itself for 7 years and then kind of forgot to appropriately plot around that. I could believe a larger ship had enough resources and spares to patch all the holes in its hull, survive about six instances in the first season of being hit with a major energy drain, fire 93 torpedoes (when it's only supposed to have 40, including the ones used for the Tricobalts) and go through 15 shuttles, but not Voyager.

The dreaded Treshold episode, obviously. It's officially non-canon now, right?

There are some horrible HORRIBLE episodes in the first three seasons of DS9 and Voyager, but I really don't feel like making a list. :p

I think one of the most stupid things in Star Trek is in Voyager. Until they get the Delta Flyer, they probably blow up about 20 shuttlecrafts. Seriously?? You have limited resources and you go through shuttles like they are nothing? It was almost a death sentence to board those... Epic fail.

Oh wait, I thought of something else Voyager related.

"Demon" - We're out of deuterium, we have to shut down half the ship and get some from this incredibly inhospitable planet, which is the only viable source.

"The Void" - Who would steal deuterium, you can get it anywhere?

Yes okay, there may not have been an nicer planet nearby with water from which they could harvest deuterium in "Demon". But did this supply problem crop over night or something? Should be filling her up every time they come across a planet with water.

Another springs to mind!

Bajoran heavy episodes of DS9, like the REALLY heavy ones, made that entire series very difficult to get into...

And speaking of VOYs "Demon" the second part was just as bad. Another (kinda) reset button episode, and for mimetic goo that mimics life but not metal somehow making a ship? yeah..

The Outrageous Okona: A lame Han Solo knockoff beams aboard the Enterprise and proceeded to bed every woman on board, including Teri Hatcher.

In the B storyline Data pretends to be Jerry Lewis.

The three people who wrote that story thankfully never worked on the show again.

Someone else already said it, but...Spock's Brain. It has to be just about the most stupid thing ever (and an almost criminal waste of talent).
But then, swathes of TOS s3 are a bit like that. Shatner's overacting and "I...am...KIROK!", anyone? Spectre of the Gun?

TNG: Geordi and Ensign Ro are out of phase and can run through walls. So why do they not fall straight through the floor? Gravity and inertia must still be affecting them, after all, otherwise they'd have been left floating in space a long time back.

Seven of Nine and the whole Borg/Federation cultural exchange programme.

Not so much stupid as (unintentionally?) hilarious: the EMH's loading of the word 'Borg', as in "Seven of Nine's Borg implants..."
I mean, what else might we assume they meant? ;-)

Not using the Insurrection cloaking suits in the Dominion War.
Voyager
Nemesis
Only having Worf from DS9 in First Contact.