Project tools are dumb because all they do is put deadlines on things. At most companies, you have a Jewish CEO asking for everything to be done now. Where I work, the programmers report to the director (or VP) of IT once a week to go over projects. Big projects are easier when split up into smaller tasks. We do have a help desk system to track tickets (which was written in house). Tickets come into the help desk and are distributed to the proper department. The help desk system is more important than project tools.
I'm working on a new file load for incoming orders using a new pipe delimited file. Seems easy right, wrong. There's 2 different order types, and 5 confirmation files going back. So I did the order load first, an ASN, a Confirmation, and a Void file going back. Now I have to work on the order load for bulk orders, and an open orders report. Lots of things, they have to be done one at a time. I call it "evolution" as we work through projects. They don't get done in a day, plus there's a ton of testing after everything is coded.