The I T manager over here wants us to convert 1 branch in our company from Win98 to Linux

Bold move, have you had anyone resouce this? It's not exactly a small task.

I would just like to know the types of problems that we will have once this is done.

One I can think of is re-educating everyone to a new platform.

Does Linux come with a Office package or can you download or do you have to pay for it.
( Office - something like MS word, Excel etc... )

There's StarOffice with is very similar to the MS Office applications.
Haven't used it myself just yet.

Does Linux come with it's own Mail program or can you download or do you have to pay for it.
( mail program - something like Outlook Express )

What happens if somebody mails you a doc from Win98 would you still be able to read if on the Linux PC.

Sorry, know little in that regard.

Best of luck to you though.