Adjust the path to the Firefox executable as necessary.
Programs that are IE-dependent will not run in Firefox, but I'm sure there are alternate versions created for Firefox. If not, try checking the Extension Room for user-created tools.
By "programs" I'm assuming you mean toolbars, etc. If you mean things like Flash, Shockwave or Windows Media Player, Firefox works perfectly fine with them.
Firefox has built-in pop-up blocking. It also blocks all ActiveX scripts from running, which generally means increased computer safety.
Firefox works poorly in IE-only websites; there aren't very many of them any more, but you'll definitely know when you come across one.
Visit the following site for tips on how to customize and improve Firefox.
I'll link you to my personal user.js and userContent.css files; they're tweaked for speed, and should make things move a lot more smoothly for you. See the above link for details regarding what to do with these files. Keep in mind that speed settings are optimized for a broadband user.
On the whole, however, Firefox is better than IE. It's easier to customize, it's more secure, it properly handles PNG images and CSS, functionality can be added to it via extensions, and it has active developers when compared to those of IE. Not to mention Microsoft is discontinuing standalone versions of IE, so if you want to get an upgrade to IE to fix the latest security holes and such, you'll need to buy a new operating system.
Er, of course you can always download it and try it.
One thing I've noticed is that there's no option to right-click on a non-downloaded image and select "Show Picture" as you can in IE -- useful if you're on dialup and stop a boggy site mid-download and then want to then view important images.
I wish I could show/hide and rearrange the toolbars and menu bars.
Those are the only things I can think of at the moment. I would be completely IE free if I didn't have to rely on an activex object on the work intranet I develop.
Also, right-click on the non-downloaded image and select "View Image" to view the image. It'll open up a new window or tab (well, my setup does) to display the image in.
Some pages render much slower in Firefox than it does in IE. (example, avensys .org)
And some JavaScripts stall Firefox for a while sometimes. (example, friendster .com's advertisement scripts)
IE is merely a frontend to the MSHTML engine, which is loaded whenever Windows starts. This may be a good or a bad thing for IE, but this also means IE will always load much faster to Firefox.
And I think the right click- show picture issue has been mentioned.
ff 1.0 and above has incremental search, which is a pretty good feature if you prefer keyboard navigation. forwardslash brings it up, ctrl+g jumps to the next instance of the string and esc exits the search.
thunderpeel, while it might not be the same, you can always rightclick the image that isn't loading and middleclick 'View Image' to load it into another tab.
I can see a reason to use a transparent gif as a background -- if you had various channels in your web site, it's an easy way to have the same patterned background in a different colour for each area.