Most of Phineas and Candace's brother/sister moments are accidental ones because for some reason, Ferb is almost never there.
On a related note, there's Candace's tendency to call just for Phineas when she needs help, even when Ferb is there and especially when he's the one who ends up saving her. Even worse, in "Gaming the System," when Candace thinks both the boys are dying, she runs to Phineas and holds him while he fizzles out, only thinking about Ferb once Phineas is gone.
On another related note, which isn't so much a tear jerker but a sweet sort of thing, is when Candace is in the boys' kiddie ride in one of the episodes. She eventually falls down a canyon after the engine sputters out... then she doesn't have another quarter to put in to power it up. She screams for Phineas to help her but who's the one who realizes shes falling and pretends to be a dancing little statue thing all just to get a quarter to save her? Ferb.
Bonus points for Ferb actually showing a bit of shock and fright at the sight of Candace falling to her doom right before he goes and saves her. Knowing that it takes so much for Ferb to show emotion is a subtle way of showing the sibling bond.
At least until the end of the series, Candace will probably never stop trying to bust her brothers, even though she'll inevitably fail and go crazy with frustration each time. Not a tragedy, but still not a very happy life.
Even sadder, even if she ever does bust her brothers or find out why the inventions disappear each time. The writers will just undo that with either time travel, memory erasing, or All Just a Dream... over and over again keeping her in an endless cycle of never knowing the truth and looking more and more insane. Though when Linda "does" see the inventions, expect a memory erasing or ironic misunderstanding immediately afterwards. The writers are almost sadist with this.
Man, Dr. Doofenschmirtz had it rough as a kid. Sure, it's mostly Played for Laughs and he's not exactly the nicest guy but...Jesus! Having to set up your own "Surprise birthday party", and spend most of your childhood as a Gnome?! Not to mention the fact that his parents never showed up for his own birth! It's kind of hard not to feel for the guy.
The part where Candace keeps picking up instruments to play for her mom on her birthday, only to have them vanish thanks to Doofenshmirtz's inator. Sure, it was Played for Laughs, but still.
It's About Time!
Doof and Perry's plot. Even though it's full of Foe Yay, it's still heartbreaking.
Buford has proven to be a bully with sentiments and does like a few of the characters - his overwhelming crying over losing his goldfish is mostly played for laughs - but it's still crying, and it's from the bottom of his heart!
Oil on Candace
Django's giant painting being washed away before his father can see it. Fortunately, his father likes the regular-sized painting he made earlier just fine.
Phineas and Ferb Get Busted!
The boys have both been heartlessly brainwashed, removing their creativity and imaginations (which may, in itself, be an example). They and Candace have been cornered by the Smile-Away sergeant, so their only means of escape are by building a bridge. Candace begs them to come to their senses, telling them that, despite the way she's treated them all summer, their creativity isn't bad but, in fact, the best thing about them and she's always secretly been proud to be their big sister. She then starts to sob and cries out "What have I done? WHAT HAVE I DONE?!". Slowly, Phineas blinks, then reaches forward to take the wrench from her hand. She looks up at him with tears running down her face. Phineas smiles and she smiles back. Granted This was all a dream, but it still shows she loves them.
"Chains On Me" in the same episode is a slow, but catchy song, about Phineas and Ferb having their creativity and imagination slowly and cruelly stripped away from them.
The Lake Nose Monster
Though it's only momentary, Phineas is clearly very upset when he accidentally betrays Nosey, his voice cracking when he pleads for Nosey to return.
Tip of the Day
"I've have an ouchie. In here." And this is right after Doofenshmirtz runs joyfully out of his room due to mistakenly thinking he had erased his humiliating incident from everyone's minds.
The ending should count for Doofenshmirtz when the De-loveinator ended up zapping his date and making her feel nothing for him. And this was immediately after an "evil love song" and Doof saying he's never been so happy in his entire life. Not to mention that he had debated using it earlier but decided to throw the remote control away instead.
The part where Perry leaves gets me every time. The normally stoic Perry looks almost driven to tears when he is forced to relocate and leave his family behind.
The one who gets me teary-eyed is Candace. She thinks it's all her fault Perry's gone. The fact we know it isn't her fault at all makes it worse.
Perry Lays An Egg
Doofenshmirtz: "She left me for that trash-talking 35-ton pile of blubber. And broke my fragile, 10-ounce utterly-too-human heart."
Finding Mary McGuffin
It's already been listed as a CMoH, but "Not So Bad a Dad After All" has the potential to reduce watchers to an absolute wreck, particularly if the watcher has experience with a divorce or daddy issues— made infinitely worse if both criteria are met.
In the room where Doof is working on his inator for L.O.V.E.M.U.F.F.I.N.'s contest, there are several pictures of scratched out inators on the wall. On one◊ he's written "I hate myself!"
This troper always feels sorry for Phineas in this episode, as we see that he is clearly uncomfortable with keeping secrets from Isabella, but has no choice but to do so, which leads Isabella to think Phineas is ignoring her and even acting somewhat selfishly for not helping fight Khaka Peu Peu. Probably the biggest thing in this regard is when Khaka Peu Peu comes towards the end, and he is forced to abandon her sadly, where Isabella's cries of "don't leave me!" pretty much cement this. In fact, this is probably the only episode where Isabella actually openly acts distant towards Phineas, and it's great seeing them resolve their issues at the end.
Most of the song is a Crowning Moment of Heartwarming, but the end says that, while Candace still loves Ducky Momo, and loved him throughout her childhood, she is made fun of because she is now a teenager. This is made sadder due to the fact that it is true in real life. Still loving something that you loved when you were a child would get you mocked and teased when you get older.
Doof finds out that Roger took 20 years to re-make his painting, and that he felt bad for ruining it. This is mostly a Crowning Momentof Heartwarming, considering how much of a Jerk Ass Roger normally is, but it becomes a tear jerker when Doof accidentally ruins it again. Then Doof gets so depressed that he tells Perry to do anything, as he doesn't care anymore.
Phineas and Ferb Interrupted
We get to see the aftermath of one of Perry and Doof's fights: Doof is sitting in the middle of his lab next to the remains of his latest Inator, hugging his knees and crying. Really takes the fun out of all the other battles, seeing this poor man defeated for the millionth time by a small animal and crying all by himself next to the ruins of his latest creation. The fact that he spends the rest of the episode gleefully convinced that Perry has had a change of heart and wants to be partners only makes it worse.
A Real Boy
Norm. Just try not to feel terrible for that lovable 'killer robot man' during this episode. Especially at the end, when it looks like Doof is about to apologize to him. Given the show's (and Doof's) track record, you know what's coming, and it's simultaneously hilarious and heart breaking to hear "There's someone I always have considered family, and that person is... Perry the Platypus!". At least he took it well... since he was wearing Vanessa's headphones and couldn't actually hear him.
Norm: Apology accepted... Dad!
The Remains of the Platypus
The sad look on Perry as he gets mindwiped and how he uses all of his remaining will to write “I fight evil“ gets me every time.
Doof gets hit by his own Truthinator, which causes him to say "Secretly I'm very lonely."
Bully Bromance Breakup
Buford and Baljeet "breaking up" over plastic. This sounds funny, and, for the most part, it is. That is, up until the song. While most "sad" songs in this show are merely Played for Laughs, we get Buford and Baljeet tearfully singing about missing each other, saying that there's a "bully sized/nerd shaped hole" in each of their hearts. Damn...
Meapless in Seattle
This list has featured a break up between a bully and nerd, a girl who loves a duck, and a bully losing his fish. All of these things are certainly sad, but nothing, NOTHING, beats the unlikely tear jerk-ness of Balloony's death. Yes that's right. They can make you cry over a balloon popping. Note that said balloon has a creepy-looking Uncanny Valley face, and that still doesn't make it any easier to see it go.
Upon thinking that everything is done for, Candace records a tearful farewell message for her mother on her phone. Yes, it is a reference to The Blair Witch Project, and yes, what she says does become a bit odd, but it is honestly, one of the most emotionally charged things she has said since her "I Know You're in There Somewhere" Fight in "Phineas and Ferb Get Busted".
Tri-State Treasure: Boot of Secrets
Candace works so hard to get a rare Ducky Momo collectible at the swapmeet, though Doofenshmirtz's latest invention causes the final item to trade with the man with the collectible becomes new again (instead of rusty). The saddest part is that it wasn't anything that could affect the show itself, and fate just felt like being mean to her.
Especially harsh if you actually collect plushies or figurines. Moments like this can be too close to home.
Perry having to stay behind to go on a mission while the Flynn-Fletcher family goes on vacation. Especially sad is Phineas' disappointment in not being able to bring Perry along.
Makes it even more depressing when you can relate to this song. Having people telling you what to think and being stressed out by society is the major issue teenagers are having these days. It really makes you want to live with monkeys!
Robot!Candace's Heroic Sacrifice. And when the real Candace asks it why it decided to save her, it simply replies, "No Jeremy robot for me."
Road to Danville
Doofenshmirtz's breakdown, as well as Perry being kicked off the bus due to no animals being allowed.
To elaborate on Doof's breakdown: He constantly repeats "It's all my fault! I'm a failure! I'm a failure!" as he sobs, meaning he actually thinks that the neglect he suffered from his family as a kid, his wife divorcing him and his daughter constantly being embarrassed by him is his own fault.
Balloony dies for real. Made worse by the fact that it's only mentioned as an offhand remark.
Happy Birthday, Isabella
After Stacy finds out that Perry is a secret agent, you can see he's upset about having to erase her mind. However, Stacy is able to invokeLoophole Abuse and Exact Words, and the two agree to keep her knowledge a secret. Perry's smile at that moment will bring tears.
Stacy: Wait a minute! It says right here in your silly little pamphlet that if your host family finds out about your agent status, then anyone who's seen you has to have their memory erased, or you'll get relocated. Perry, I'm not part of your host family! I know, I know, it's a technicality. Look, I don't want Candace and the boys to lose you, but I also do not want my mind erased. I'm on the last ten minutes of that "Grievance" movie, and I don't want to have to watch that whole scary mess again. So, uh, can we just keep this a secret?
(Perry grins and tips his hat to Stacy)
Isabella's song about how she just wants time with Phineas for her birthday. If you've spent a birthday away from your significant other, it is particularly heartbreaking.
Doofenshmirtz feeling left out while Perry and Lyla are working together.
Doofenshmirtz: This is why I'd rather not make friends. They find someone else, and "Bam!" You're alone.
Cheers for Fears
The entire "It's All About You" sequence.
Doofenshmirtz shows up to give his father their old lawn gnome back, but unfortunately it ends up breaking and Doof ends up leaving, feeling sad that he failed to impress his father (and that Roger once again gave his dad something better). However, Doof's dad then notices that one of the shards of the broken gnome ends up showing it's code, and Doof's father then accepts his gift by gluing it back together. His father actually appreciated something he did, but Doof will never know that.
Specials and Miscellaneous
Phineas and Ferb Christmas Vacation!
The heartbreaking yet beautiful song entitled "Where Did We Go Wrong?", especially when you consider the fact that Phineas is hardly ever sad.
Jeremy sulking quietly in the snow. It's always when a secondary character gets enough love to appear in a group scene...
Phineas and Ferb Summer Belongs to You!
Watching Phineas give up hope on the island. This kid, this ever-optimistic kid who's never given up on anything before, just completely fall apart, realizing he doesn't know what to do.
"We could...we can...we can...we...we...we can't..." Hearing one of the biggest and most lovable optimists in modern television say those two simple words is nothing short of heart-gutting.
As well as the scene just before it. Isabella never cries, but she did then.
"The City of Love". It's the culmination of how many seasons of Isabella's frustrations and Phineas' Freaking.Obliviousness. Her plaintive little voice, and the fact that he's still oblivious as she sings this right in front of him are just sadness on overdrive.
Vanessa leaves Ferb standing alone at the top of the Eiffel Tower holding a rose that he was going to give to her. Not quite tear-worthy, but still very sad.
In particular, the part where Candace tries to talk to Ferb about it only for Phineas to divert the attention of both of them is pretty sad.
"Only Trying to Help" is one of the most depressing songs the show has ever had. If you already feel bad for Candace and Isabella, then listening to them explain their feelings of rejection while watching flashbacks of what they have been through is just downright tugging at the heartstrings.
Doofenshmirtz gets sidetracked for a few moments while he is introducing himself to the supervillains by the fact that no one wishes him well on his birthday.
The Dwindling Party nature of the plot, and the reactions of the remaining characters being progressively more tear-jerking with each zombification.
The scene where Isabella finally confesses her feelings to Phineas in particular hits pretty hard, as not only does Phineas pull a Heroic Sacrifice to protect her before he can reveal his response (which has her even visibly holding in tears when she watched it happen), but it is also implied that they forgot that moment as a result of being zombified.