Okay going to go off on a tangent before talking about some of my favorites:
I fucking hate SCP's 999 and 682; I know they both came out early in the cycle, and they're a big part of the sites history. But I fucking hate them both due to the standard they set for newbs. Talk to any fandom of the SCP and ask, "Whats your favorite SCP other then 173, 999, 042(I think that's the doctor), or 682." They'll either respond with another Scip from the game, or just be like, "They are others?". Then when they try to write, they write another 173 or 682. And its getting to become more and more obvious the more and more kiddies sign onto the site. I don't care for 999 because it seems unfitting on a horror and oddity website, that and its free to roam around the facility and saves people?
lolwut Then you have 682 who is just the ultimate Mary Sue monster that is only there for one reason: so you'll never have an SCP as powerful as 682, that's it, so they wouldn't have to always deal with uber-powerful beings or monstrosities and I'd like to call some bullshit on that.
Now onto my personal faves:
674 Nes Zapper: I won't spoil the payoff because it is fucking awesome, but I will say this. You can kill anyone you want with it, its like a real gun but with a few clever restrictions.
1295 Four Angry Old Men of the Apocalypse: Alright I will spoil this because it makes the whole thing a much better read then having to scroll through hours and hours of theories, that and its pretty obvious. So this SCP is about the Four Horsemen of the Apocalypse now aged beyond belief at a diner they constantly eat at, at set hours of the day; why? Because during the Trinity Project (I think it was War) saw the atomic bomb and though that was the signal of the End Times... well it wasn't and as their punishment from whoever controls the universe they have been banished to the Earth until the actual End Times begin. Until then they're left in a diner to bicker at each other.
583 Choking Tapes: Just read it.
1425 Self-Help from the Stars: Alright I will be honest, besides the three others below this, this one got to me. This was the second SCP I read that actually got under my skin and scared the shit outta me. This SCP is basically what happens when a memetic object is a able to take over the world, what it describes is both Lovecraftian and something you'd see on the news. It is a very, very good read and I always recommend it as the first SCP anyone should read other then 173.
1981 Ronald Regan Cut Up While Talking: Its scary, do I need to say anymore?
1733 DVR Basketball: Alright guys, this is one is pretty good on its own. Just read it, I read it early on when I was starting to read the site more (basically I read it on my lunch breaks at work (before I quit)), and needless to say it got me more interested in the site.
2006 Too Spooky: I won't ruin the payoff, but this is how you do SCP-999 the right way. Its still adorable, but not taking it seriously is still a fucking danger to us all.
835 ...: *BBBAAAUUUUGHHHH* *BBBAAAAUUULLFFFFGGG* *AHHHHHHHH*