Chessbase with megadatabase is the way to go. With a comp program for analysis
PGN Viewer

Try this CM :) http://www.chess.com/analysis-board-editor

In Scid, you can create a database in its native format si4 or somesuch ... once you've done so, you can import pgn games into that db. You can copy and paste pgn into and maybe even out of regular scid databases, too, which is something that only Scid allows, as far as I know.
Scid won't work with raw pgn - at least not with full functionality - neither will most other DBs as far as I know. I personally favor Scid over Chessbase, but only because I can play against the engines from within scid, and CB doesn't seem able to do that - it lets you "send position to Fritz" or somesuch, which is not the same and requires that you buy an engine bundle as far as I can gather. This is SOOO useful - you're playing through a game, one side resigns, you'd like to test your technique against strong opposition, but your local expert or master is not at your beck and call, so you just play it out against an engine.
But yes, Chess.com does have an analysis board feature: http://www.chess.com/analysis-board-editor

Chessbase with megadatabase is the way to go. With a comp program for analysis
I think if I start doing tourneys I will go that route. What do you recommend for the computer program for analysis? By the way, I have a Mac -- but you can buy PC virtual machine emulation applications (Parallels, VMWare, etc.) to allow you to run PC software, so I'm sure it is fine. I don't know if you know anyone who uses Chessbase with a Mac?

@jlconn: Thanks. ScidvcMac may be powerful, but it is NOT user-friendly at all. Horrible. I'm not 100% crystal on what you are saying the problem is with Fritz, but I was under the impression that Fritz was a complete package including engine and GUI. I've never heard anything negative about Fritz.
By the way, you took care of donald in short order. I'm trying to practice the open Sicilian a little like you suggested, so I copied the PGN to review.

No problem with Fritz
The problem is ChessBase, and it's not really a problem - unless I am mistaken, and I very well may be - if you have only purchased ChessBase, there is no way to play over a game/game fragment in a database, get to a position, and tell ChessBase you want to play a game against an engine starting from that position.
This is a great training method, and it's easily done in Scid. If it's possible in CB 12 or earlier at all, I have no idea how it's done, and it isn't simple, and it probably lacks some abilities that Scid gives me.
Scid takes getting used to, but in my opinion it's easier to understand than CB, and I've heard CB is easier than Chess Assistant - but that's all a matter of taste anyway, and with the addition of hearsay in the case of Chess Assistant.

I believe you can download houdini 1 for free still. It is much stronger (and freer) than fritz. I'm not sure about mac vs. pc as I have a pc. I have chessbase 9, megadatabase, and houdini and I can pretty much do everything I want.

Hmm.. the best made to run natively on the Mac is supposedly
http://www.hiarcs.com/mac-chess-explorer.htm
Macs and their native software are known for being user-friendly and idiot-proof. I need that. That being said, it is probably not as powerful as Chessbase and probably has like 2 million games in the DB instead of, say, 8 million. As someone who will never be a pro chess player, I'm not sure what kind of difference it will make...anyway, I don't need anything right this minute. I don't evern know how to respond to 1.e4 with 1...e5 but I'm told it's a beeeeatch.
I'll probably end up going with chessbase though...I'm sure i can figure it out...

I believe you can download houdini 1 for free still. It is much stronger (and freer) than fritz. I'm not sure about mac vs. pc as I have a pc. I have chessbase 9, megadatabase, and houdini and I can pretty much do everything I want.
Well, the thing that is good about Fritz is you can use it to (now this may not be anything an NM cares about -- but for someone like me) play the computer, and it has a built-in coach. It will, when prompted, give you hints (e.g., you should think about guarding d4). It will even give you a suggested move if you have no idea what to do. That can be nice for a beginner or intermediate type of guy....
Someone who is trying to become a Candidate Master right now was telling me about MEGA. Sounds great...

Is there a PGN viewer built into this site? I have some lines with variations for an opening and it's variations. What's the best way to store and view the PGN files so you have them in front of you, showing the variations that you can move through, when playing a turn-based game?
I have Scid (well, I actually have Scid vs Mac), and can load in the PGN, but I don't know how to make it show the variations as people do here (e.g., when they show the answer to the Daily Puzzle and variations). Is it even possible with Scid? Maybe I should be using a different program?
I'm just asuming your talking about analyzing completed games and not on going games ???

Not analyzing, exactly....
Say a game between two GMs ends with resignation in a position where one of them is a pawn up - pretty much any game from the Alekhine v Capablanca match, for instance.
You play over that game in your program, and reach the end. As a non-GM, it's a good idea to test/train your technique. Can you actually win that position against best opposition? So in scid, I simply go up to game, new, from current position, then set the time limit for each side, etc. and off I go.
I don't believe that functionality is built in to CB. I would assume it is built in to one of their engine bundles, and I believe you can "send the game to Fritz" and I assume that means play it in Fritz ... but to my knowledge, I cannot do the same thing without starting a new program in a separate window. As I said, I could be wrong, and if so, esp. if it can be done in CB 12, I'd like to know.

I wasn't talking about "analyzing" games at all. I was talking about when you have an opening repertoire for, let's say, responding to 1.e4 with 1...e5 (for example). I have a PGN file with pre-prepared lines (a repertoire essentially, like you could find in an opening repertoire paperback book). You can make the lines yourself before you play your game -- maybe you choose some lines from wikipedia or a paperback opening book. Then, when you are playing the game, your preferences are built-into the PGN file. For example, after 1.e4 e5 2.Nf3 if I forget what i normally play in this situation, i click on it and it shows 2...Nc6 is my preference (which I put in before the game ever started). So no analysis is not being done. It's like looking at an opening book. Hopfefully that made sense. It's static.. not dynamically analyzing the game. That's not to what I was referring.

Right - it was a side issue.
The suggestions of DB programs in the first place stems, I think, from the fact that we all share the same opinion ... any DB program makes it easier to do what Chicken_Monster wants to do than does the Chess.com editor.
Again, that's a matter of opinion. If you just want to quickly annotate a pgn to throw into a forum or something, the editor may indeed be the way to go.

Chesstempo also has a PGN viewew I found. Works great for loading your opening PGN file, with variations, then going through it to check out the variations.
XBoard is available as OSX App, and can be used to examine or edit PGN games including recursive variations. (I suppose this is the way you store the opening lines.)
After loading a game you can step through the moves of its main line using the arrow keys, and any variations will be shown (as text) in the Comment window. Right-clicking a variation there will then promote it to main line, so that you can step through that. Clicking the Revert menu will then recall the original main line. This way you can navigate through the entire variation tree.

XBoard is available as OSX App, and can be used to examine or edit PGN games including recursive variations. (I suppose this is the way you store the opening lines.)
After loading a game you can step through the moves of its main line using the arrow keys, and any variations will be shown (as text) in the Comment window. Right-clicking a variation there will then promote it to main line, so that you can step through that. Clicking the Revert menu will then recall the original main line. This way you can navigate through the entire variation tree.
I've heard of Xboard. Thanks. I can try it. I believe it may be the non-commercial free version of:
http://www.hiarcs.com/mac-chess-explorer.htm
That you have to pay for, but I heard it was the best native application for the Mac that compares to Chessbase. Do you know anything about it, or about people running Chessbase on a Mac? Or other software for Macs?
Is there a PGN viewer built into this site? I have some lines with variations for an opening and it's variations. What's the best way to store and view the PGN files so you have them in front of you, showing the variations that you can move through, when playing a turn-based game?
I have Scid (well, I actually have Scid vs Mac), and can load in the PGN, but I don't know how to make it show the variations as people do here (e.g., when they show the answer to the Daily Puzzle and variations). Is it even possible with Scid? Maybe I should be using a different program?