Does time machine work well for hd upgrades? Looking to go to ssd but don't want to lose things like custom plist settings, init.d items, .profile items and all my brew installed items. Is times machine going to help me here or do I need something like superduper?
Carbon Copy Cloner is my recommended way to migrate a hard drive. It's like SuperDuper, but free. Does enough to get the job done.
I wouldn't rely on Time Machine. There's quite a bit of stuff that's excluded from Time Machine by default. And it doesn't always follow symlinks around your file system properly when backing up. For example, I had trouble with it backing up duplicates of a few files installed by Homebrew instead of the symlinks that they were. It de-linked them. That could wreak havoc on your Homebrew install if you were to restore from it.
Unless you are doing unusual things, Time Machine is the normal Apple-supported manner of restoring your entire Mac should the internal hard drive fail. In this case, you still will have the old drive and can connect it to do a sanity check using an inexpensive SATA to USB adapter.
I figure I've got larger problems if the tools I need don't get backed up properly and Ian has linked to a nice question (ahem) that will let you know before you start if Time Machine is capturing the data you need. Using it might be a great test before you lose your primary hard drive and lose actual data.
You could also implement Carbon Copy Cloner or Super Duper and test them as your backup solution, but why not use this as a "dress rehearsal" for your chosen backup strategy? (no matter which is best for your needs)