An app I myself can't do without is F.lux, it does wonders for my eyes. Just don't turn it on for the first time at night, you'll see orange people! I never notice it these days, and miss it instantly when I view someone else's monitor at night.
I love the functionality of ClipMenu, and missed it when it stopped loading for some reason (I blame the cats of the house.)
ILoveStars is great when you're building smart playlists, I used it a ton this past Christmas when I was sorting out all my Christmas music into things I want to listen to, and things I could delete and not miss.
LittleSnitch. Goes without saying.
I go back and forth between iChat and Adium. I do like Adium, but I went back to iChat recently for some reason. I'm not sure why that reason was.
Twitteriffic2 > Twitteriffic. It takes a little getting used to, but worth not getting those stupid timeout messages all the time.
For my line of work, I like Transcribe! over ExpressScribe, although I may be in the minority there.
Transmission. Thou Shalt Use No Other Torrenter.
I love Minuteur for a stopwatch, but there may be other, better ones out there. I just didn't like Apimac Timer that much.
AppCleaner. It's so simple, doesn't run all the time like some other cleaner app I had, and lets me save files from being deleted if I wish to save them, when I'm deleting the associated app.
TextExpander. I haven't used this a ton, but I appreciate it when I do use it.
Get Lyrical is great. Absolutely wonderful. Saves a ton of time if you're into keeping lyrics on-hand. Hands free, or you can choose to import lyrics on a by-song basis if you like.