I don't think TM is happy with you swapping files manually, but I can't say for sure. Even if it's OK, you'll have to start from your DVD and restore your HD, that takes time - a lot of it - which you never seem to have, when you have a melt down.
The free version of SuperDuper will back up everything, including system files.
The paid for (cheap) will do incremental back ups, which are much faster, which again will encourage you to do it more often.
To me it's a no brainer, but then I suppose I'm a back-up-aholic
on the other hand - I seldom cry
In case you have a boot camp partition, you'll need Winclone for that one, it's free!
Their website has disappeared, but the app can still be found on cnet