Dragonfly 2 would probably be my favorite/most used Spyderco. I picked up the yellow SE H1 version ~7 years ago and it has seen the most action. Some abusive for such a small, light, linerless knife. It has held up very well.
Eventually, the yellow DF blade has gotten a little shorter and doesn't seem to sharpen up like it used to. Recently picked up a plain edge version to retire the old one with.
I like quite few, but I always end up coming back to the Manix (have yet to try a Shaman though). That, and I have a thing for the fully serrated Dragonfly. It adds so much utility to my EDC while going unnoticed in the corner of my back pocket until needed. Also, the entire salt series was a game changer IMO and deserves a mention.
So many great Spydercos out there, but these two resonate the strongest with me:
Para 3 (S30V, S35VN, M390, REX 45) - So much fun to use ... and so much fun to customize. For example, I recently put skinny-mod Micarta scales on the S30V, swapped the red G10 scales from the M390 to the S35VN (Blood red scales and black DLC blade - looks fantastic), put dark brown smooth dress Micarta scales on the M390 (so clean!) and dyed the desert tan G10 scales (originally on the S35VN) to Ranger Green for the REX 45, now dubbed Ranger Rex!
Native 5 (S90V, S35VN, Maxamet) - It's the most aesthetically pleasing Spyderco in their lineup. Balanced and strong. Feels fantastic in the hand (though you can say that about almost any Spyderco) and it sits lean in the pocket. The CF version is my favorite knife... period.
I love customizing my knives, but particularly the Para 3. It just lends its self to it, and with so many aftermarket options you can let your creativity roam. I learned a valuable lesson, though, you need the right tools. Using the wrong tools, or cheap tools, will cause you nothing but headaches.
I also have the Lil' Native, Shaman, PM2 and Manix 2. Great knives, but not at the same level as those two listed above.
One final thing.... some day Sal and Eric are going to release a compression lock Native 5 and it's going to absolutely set the knife world on fire. The beauty and functionality of the Native 5 coupled with the fan-friendly compression lock? Sign me up now, guys.
My favorite is the manix2 in 20cv in red g10. A year and half of use . It's a tough one ,only regrets ,a little bit of a pocket hog . Says like a razor with a weekly date with the golden stone. It was my first 20cv blade .
I think my favorite platform is the Delica. I'm not a fan of the current gen's steel liners, but in the end it's the knife I grab the most. The Wharncliffe Salt is a linerless variation based on the Delica, and is the primary knife I carry at work on a daily basis. It just fits my hand perfectly.