Below are my current top picks for freeware Internet applications for Windows (and/or Linux). Choices were made based on features and usability.
1. Download Manager: Free Download Manager
Free Download Manager is a powerful, easy-to-use and absolutely free download accelerator and manager. Moreover, FDM is 100% safe, open-source software distributed under GPL license.
One of the most useful features of FDM is that you can set and choose three (3) Traffic Usage Modes: Light, Medium, and Heavy. You can set it to Light or Medium, so that you can surf the net while downloading files without noticing any browsing slowdowns.
It also integrates a BitTorrent client (for downloading those Linux distro ISOs), so you have one less client to manage.
2. Email Client: Mozilla Thunderbird
Mozilla Thunderbird is a cross platform stand alone mail application using the XUL user interface language. Aside from email, it also supports RSS news feeds and newsgroups.
This is a great email client, especially if you currently dual boot Windows and Linux operating systems on your PC. You can set a shared profile wherein all your email and feeds are placed in one common area, for both Windows and Linux.
3. FTP Client: FileZilla
FileZilla is a powerful FTP-client designed for ease of use and with support for as many features as possible, while still being fast and reliable. This lets you upload or download files to and from your FTP server in a flash, with no complicated setup routines. A portable version is also available.
It's simple to use, and almost doesn't need any configuration. And not to forget fast, and frequently updated.
4. Instant Messenger: Pidgin
Pidgin is a multi-protocol instant messaging (IM) client for Linux, BSD, and Windows. It enables you to set all your IM accounts (GTalk, Jabber, Yahoo, MSN, AIM, ICQ, and more) into one single client. A portable version is also available.
5. IRC Client: HydraIRC
HydraIRC is an open-source IRC client with an attractive and easy to use interface. It supports DCC Chat and File transfers, Multi-Servers, Dockable Floating Windows, DLL Plugins, Channel Monitoring, Message Logs and more.
This has a similar interface to the popular (but not free) mIRC. The portable (ZIP) version would be handy for USB flash drives.
6. Jaiku Client: Jaikuroo
Jaikuroo is a desktop client for presence updates on Jaiku.com. This requires MS .NET 2.0 Framework. It is simple and fast, and doesn't hog your monitor real estate.
7. RSS News Reader: GreatNews
GreatNews is a free RSS news feed reader that features fast reading, news highlighting, and the ability to save & organize articles. Absolutely no adware/spyware, and doesn't need .NET or Java runtime.
Although you can use Thunderbird also as your news feed reader, GreatNews goes a step further by providing great features, such as Feed Groups, Labels, and News Watches. Feed groups let you arrange feeds according to topic, while Labels let you tag individual feeds. For News watches, you can set keywords that would highlight feed entries, for easy visibility.
It's a shame that GreatNews is not available for Linux. For dual OS booting, your only option would probably be to use Thunderbird (or of course, an online reader).
8. Twitter Client: Twhirl
Twhirl is a desktop client for the popular microblogging service Twitter. It allows you to post short 140-character updates about what you are doing, as well as following your twitter friends and read all their updates, replies anyone sends to you, and direct messages to your account. This requires Adobe AIR.
Twhirl is full featured and fast, and even lets you cross-post to Jaiku and Pownce. You can also fine-tune the downloading of updates, replies, and direct messages to your taste and needs.
9. Web Browser: Flock
Flock is a cross-platform social web browser based on Mozilla technologies. It has integrated support for online social applications (such as Facebook, Flickr, Twitter, and YouTube), Media sharing (Photobucket, Picasa, Piczo), blog posting, Bookmark sharing (del.icio.us, Magnolia), and most recently, Web mail support (Gmail, Yahoo).
If you use some or a lot of the above-mentioned services, Flock will definitely be a time-saver. A version for Linux is also available.
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