My only regret with this macbook is that it cant play Couter Strike 1.6, Source and Day of Defeat: Source but i guess i can live with out that lol.
Sadly, the Counterstrike engine was never completely ported to Mac. Lucky for you, you have a new MacBook... if you want to install BootCamp, and install Windows on your MacBook, you could run it. Depends on how bad you want to play Counterstrike.
Q1: Media players... you hate iTunes? Worry not, there are alternatives... search
www.macupdate.com or
www.versiontracker.com for mp3 audio players.... one of my favorites is Audion, although, it isn't supported anymore... but there are plenty, including Mint, and quite a few others...
Q2: You deleted the QuickTime app.... which... is kind of a problem. lol. Search for "QuickTime Player.app" on your drive... otherwise, you'll have to do some fooling around using an app called "Pacifist" to yank it from your system disks... doable, but annoying.
Q3: If you download FireFox for Mac (
www.getfirefox.com ), not only does FireFox have a great built-in popup blocker, but there are great free plug-ins that address other popups, too.
Q4: Virii and CrapWare: You're probably just fine. There isn't much to worry about in this department. Although, be wary of Microsoft Office documents (if you run Office), as they can contain macro viruses... but basically, nothing to see here.
Q5: Hidden folders... if those folders start with a "." then they will not appear on the Mac. Rename them without the period and you'll probably be fine.
Q5: WinRar... This is not really my expertise, but if there's a compression format, Stuffit will do it. It's been around on the Mac forever....
http://www.stuffit.com/mac/deluxe/
Also, I'm pretty sure Rar is actually supported in Mac OS X via the command line.... Hmmm... I'm sure there's some free utilities out there.
http://www.macupdate.com is your friend.

All your software needs.
Enjoy your new Mac!