Id say it depends, if its business related id say higher a security expert ASAP and have em come set you straight. It WILL be expensive. The problem here is probably "most" of the advice we could give you would be over your head, not to mention in a "rooted" case you need to do about 3 fucktons of searching and analysis. You need to locate the vulnerability they got in with in the first place, patch/fix it, look for backdoors in everything....its just a LOT of work. A lot of it that takes a good bit of knowledge to go with it. Their are SOME things you could run like VICE that MIGHT show if you got a rootkit running. But really if this impacts a business id say bring in the professionals, and if you really want to prevent/detect this stuff in the future on your own to start reading a LOT of books. If this is just some sites you have set up for "fun" id suggest starting over from the base up. (fresh install of everything), the issue being with this that you still wont know how they got in, and they can/will just re-exploit the hole if they want too. Again for this kind of thing you can try running a dork/sqli scanner on your pages see if they cant find the hole(s) and fix them yourself, but that will(at least to fix them) require knowledge on your part.
All of that being said, this is not an area of expertise for me, im sure others here will have other sage advice for yah, but i do want to iterate once more: if this is for a business, hire a professional. Even if you have the knowledge to fix all this on your own, its always a good thing to have an outsider look over your security to see if they cant find something you missed. One final thing:no program can find everything, and dork/sqli's are just the normal "easy" way in, they could have gotten in in a number of ways, just that its a place to start looking.
