I have to do a lot of work regarding setting up of network in my new office premises.

In my office, some 20 number of desktop computers connected in an ugly manner. And we are shifting the office to a new building.

This time we are having a lot of hardware(new as well as old systems) to configure the new infractstructure.
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1. There is one windows 2008 server machine - with 5 client access license
2. 16 nos of windows Vista Desktops
3. 4 wireless access points and 30 wireless adapters
4. One multifunctional printer with wireless access too
5. two medium duty network printers
6. 2 light duty network printers
7. 10 usb printers
8. 6 windows XP desktops (dual core machine)
9. 5 old Pentium IV machines
10. 20 laptops with windows vista
11. Two Pentium III IBM computers
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Broadband internet connection is there, in which the internet is shared by squid proxy in the multi homes PIII machine

I want to build a windows/samba domain controller network access

But there is only 5 CALs for the server OS. Therefore, I have to setup a samba server which should co-operate with the windows 2008 server (member server?).

In our office premises, 10 cabinets are there for officers, one computer room, and other people are sitting in different rooms (about 4 persons per room)- Total about 40 staff

Which is the best way to use wireless as well as wired network with samba

Sounds like a consulting job. Way more to the question than what the information you have provided allows to be answered here. The networking/wireless question is somewhat separate from the samba question. You apparently are using the Windows server, but don't have enough licenses to go around, and want to supplement that with Samba. You could make the Samba work as a BDC to the Windows PDC (my terminology may/may not be dated), but then you are still restricted by the number of licenses. If you make the Samba server completely separate, then you have a split in work flow among office members. You could dump the Windows server and just use Samba, or you could have the Samba server mount a share from the Windows server and connect people by indirection (but that could be dicey).

A lot of this depends on your work flow -- what people are doing in the office, and what they are using the Windows server for, etc. If there is no compelling reason to keep the Windows server (e.g. proprietary software that only runs in Windows), and you are comfortable with linux/samba, you could save a fair bit of money and complexity by just going with a linux server as your central node for the whole network. No way of knowing without more information and back and forth questioning.

Yes it comes to my point

I will use the Linux machine with samba and use the windows machine for serving some widows based accounting software and use the share of windows machine.

And next, the networking. Shall I use the same network for the entire wired as well as the wireless network? I know wireless network is not reliable and is slow.

umm, I think wireless can be perfectly reliable, its just slower than wired. Typically, these days, wired runs at least 100Mb/s, sometimes GigE. In comparison wireless may seem slow, but that depends on what you are doing. It would be unbearable for a graphic arts shop with all the large files they share. For a business office sharing occasional word documents and doing email and web, it would probably be more or less alright.

Since you already have the gear, go with it.

If you have the finances to do it, and want better performance, you could go with wired, but you would then have to buy more switches and run wires. Wiring can get somewhat expensive, depending on your layout, your location, and the regulations (type of walls you have to go through, asbestos issues in older buildings, fire containment with regard to running wires, how the wires are laid with respect to lighting & electrical, etc.)