i eventually build my own bitcoin server to handle my transactions. thanks for last downtime it's forcing me building my own server
Honestly, if you're relying on someone else then you're already going down hill.
Small application/not many sales? Bitcoind.
Large application/lots of sales per second? Custom developed bitcoin-interfaced program that can actually handle and raise events within your code, unlike bitcoind. Will take awhile to actually implement stuff correctly (And, believe me, you'll want to test it like no tomorrow when dealing with money), but, I think the majority of us can agree that for large scale operations, nothing beats specifically tailored software.