Will Ubuntu affect my Windows applications?

Ubuntu will not interfere with your Windows installation, as Marco has said.

To elaborate a bit more on the methods of installing Ubuntu:

Wubi install: There's an autorun and a Wubi install file on the LiveCD. This will install into Windows as a virtual Ubuntu drive that you can boot into. You will get a choice of which OS to run when you turn the machine on. Reverting to a Windows only machine is as simple as booting Windows and uninstalling Ubuntu. If your hard drive is badly fragmented then the virtual drive will be spread all over the disk, possibly impacting performance slightly.

Install alongside: The Ubiquity installer will automatically resize your Windows partition to make room for a Linux partition and a swap partition. This is the best scenario since you are running Ubuntu the way it was meant to run - on its own ext4 formatted partition.

You should back up all important data before you proceed with any installation. If bad things happen (eg power failure while the partitions are being resized/moved) then it's mighty comforting to know your data is still safe.

It's probably also a good idea to run chkdsk on your NTFS partition, and to defrag it before you proceed. It can make the difference between a simple straight forward install and a nightmare that takes forever. Resizing the partitions can take a long time if the data is fragmented all over the drive, and the operation has been known to fail badly if the filesystem is damaged (and Windows doesn't check for it unless the machine is forcefully powered off).

There's a third method that you might like to consider: installing to a USB thumbdrive and booting off that. An 8Gb thumbdrive is large enough to start with, and you can boot off it on almost any machine that will support USB booting, which is most if not all modern machines. This does tend to take much longer to start up, but it's a real install and doesn't run too badly once it's booted. I've heard of people running their machines this way after the hard drive failed, until such a time as they could get it fixed or upgraded. You might consider doing an install this way to get some idea how the advanced partitioner works: It won't changing anything at all on the hard drive as long as you are careful to put he grub bootloader, the ext4 partition, and the swap file on the thumbdrive.

Some reading for you:
https://help.ubuntu.com/community/Installation
https://help.ubuntu.com/community/DualBoot/Windows

Chris.