I recommend Duke 3D too. Don't forget to check out all the cool mods for it, especially Duke Plus.

The best $5.99 is all subjective and what one person really likes another may think is the worst of choices.
So, with that in mind I would suggest Giants: Citizen Kabuto. It is a fun game to play and has a good (i.e. silly) storyline and the switch between different characters throughout the games adds to it enjoyment.

If you like pinball, then Pro Pinball: Big Race USA is hands down the best pinball simulator I have ever played. It's only one table, but everything feels right and it's a really fun table to play on.
However, if you want another Fallout-style game, then Arcanum of Steamworks & Magick Obscura is your best bet.

Freespace 2 > Arcanum = Duke Nukem 3D
In my opinion, of course.

Divine Divinity is the best RPG on here after the ones you own.
Arcanum is a love it or hate it RPG. Watch a video or something of it first. Ditto: Vampire: TMR. Opinions are very divided on both of them.

I would go with Divine Divinity, Sacrifice or Empire Earth personally.

Hehe, how should you even compare games from different genres?
Any Realms of Arkania would be the best D&D game.
The best RPG probably Fallout or Fallout 2 - but I didn't play Vampire yet and Septerra Core much.
The best tactical game Commandos
The best strategical game is difficult, since Stronghold, Lords of the Realm and Empire Earth all would have a different setting. Stronghold if you like a realtime medieval setting; LotR if you like a turn-based medieval setting; Empire Earth if you like a "good old" RTS.
The best economical simulation Capitalism Plus
The best trading simulation ties between Port Royale and Patrician 1+2
The best society simulation (Settlers like) The Nations Gold
The best platformer Duke: Manhattan Project
The best FPS - no idea, maybe better invest 9.99 for Painkiller - if your PC is good enough - else I can't say since I didn't play Kingpin and Messiah much or at all
The best genre mix - Giants
The best Action RPG - Lionheart
The best Adventure - Gabriel Knight or Simon the Sorcerer 1 or 2 for classical adventures, some Myst game (or sequel) for render adventures
The best chess simulation - Battle Chess SE (but if you can afford it, take the Chessmaster 9000 if you don't play Xiangqi)
The best "do-missions-in-a-house-where-you-anger-inhabitants" simulation - Ghost Master
And then there are some genres I don't know like combat simulation, pinball simulation, etc.

Oh definitely great call on Empire Earth. That's a real RTS gamer's RTS game. Is there another RTS game that even comes close to the scope of that one? From the dawn of man to the future. Pretty nuts. It's a history buff's dream. The total war and age of empires games are the only other thing that are in the ballpark for me (at least in terms of traditional resource-gathering games). I never met an RTS player who didn't love EE. Some more casual types thought it was too complex, though.
Last time I played EE was after my second semester in grad school had finished. I realized about a week had passed by the time I stopped playing. My room was stacked with pizza boxes, empty bottles, and cigarette butts. Good times. Medieval: Total War was another life-destroying RTS game for me. I don't get much of a chance to play them anymore. Might today. Snow day. Just finished shoveling.
Sacrifice generally gets good to good-mixed reviews so I'm in the minority here, but I hated it. It reminded me of the recent spate of "console RTS" games (even though I know it came first). I found it relatively simplistic.
^ I think Lionheart was terrible, esp. with character class balance. You really have to play a fighter class or you get mauled in the last half of the game, Divine DIvinity is faaaaar better in the action/rpg class. I really wanted to like LH, but I think they butchered the concept and the gameplay. Critical concensus is generally that it's quite poor.
Septerra Core is quite good if slightly generic, but it's basically a JRPG/console RPG from the ps1 era (on the PC)- it's not a PC style RPG which disappoints some people. If you like FF7-9, you'll like it. If you don't, you won't.

Arcanum, Die by the Sword + Expansion (make sure to grab Hazzard's graphic overhaul mod to spruce up the game!).
I, myself, would not really recommend VTM: Redemption (or as I like to call it "The Not So Riveting Journey of Edward Hamhands and Friends").

Simple answer - ALL OF THEM.
More complex answer - The ones YOU like the best.

This is pretty much the only answer you need to go with. Pick your favourite of the bunch, not anyone else's.

If you like Fallout you should love Arcanum. Great games

Freespace 2 is easily one of the best titles in the catalogue. The fact that it's $6 makes the choice a no-brainer. You'll want to get Freespace 1 as well.
The Fallout games are the other obvious choice, but you already have them.
Other top classics in the catalogue in the $6 range are Sacrifice and Duke Nukem 3D. The MDK games are pretty fabulous classics too.

Easy, Empire Earth 2! :)
As an aside... YOIKES! It's only $5.99? Why haven't I bought that one again, yet? :)
My other no-brainer that nobody has mentioned yet is Descent 3.

I think I need to get new glasses, I can't see Arcanum on that list.