Please note that this guide is subject to change (i.e. a lot more information, details and probably images).

This is a guide I made to explain why your Saints Row 2 is faster than normal, as well as how you can try to fix it.

First of all, this speedup bug happens on all systems except XP and it's not for everybody and for every PC, some may not have it, but most of them do.
The reason Windows XP doesn't have it (that is, it's uncommon, not that it is guaranteed not to happen) is because of old technology, which is a bit on par with Xbox.

Saints Row 2 speeds up because you don't have a CPU that runs at exactly 3.20Ghz, which is pretty much the Xbox's equivalent. As long as your CPU is at that frequency, your game will run smoothly at normal speed.

Sometimes, even if you have 3.20Ghz and you're very sure it is exactly at that, your game will still speed up. This is because frequencies change due to various reasons (voltage, over-clocking, auto-config, etc.)

Also, it doesn't matter if your CPU has more than one core.

And please note that the speedup bug is not related to FPS at all, so VSync and frame limiting won't help at all.

On to the solutions...

There are actually various solutions, maybe even more so. For now, I'll just show you some of the well-known ones:

Cheat Engine

One of the ways to try solving this problem is using CE's "Speedhack". Here is the link for Cheat Engine: http://www.cheatengine.org/ (Just go to "Downloads" and install the latest one.)

To use CE's Speedhack, all you have to do is, while Saints Row 2 is running, start CE, then click on the little flashing icon to open up the process list. If you have your Saints Row 2 running, you'll see "sr2_pc.exe". Choose it.

Now, just click on "Enable Speedhack" and choose which speed you want it to be, for example, 0.95, which makes the game run at 95% of its speed. Don't forget to click on "Apply".

The problem with CE is that the cutscenes will also be slowed down, so the dialogue, animation and timing is not accurate.

Powertools

Courtesy of Minimaul and IdolNinja, Powertools is one of the well-known solutions for anyone that plays SR2 on Windows 7 (or Vista) with the speedup bug. Powertools is almost the same as Cheat Engine, but does not change the cutscenes at all, keeping them at their original, accurate speed.

Here is the link for PowerTools: http://saintsrowpowertools.com/
Here is the Beta version of it: http://saintsrowpowertools.com/oldbeta/beta.html

What's the difference? The first one is non-beta, you'll have to set up the speedhack manually. The second one is a beta version that attempts to set the speedhack automatically; it is not very accurate.

In case you're having trouble using the manual version, you could try the Stop Watch: http://idolninja.saintsrowmods.com/sr2/tools/Powertools_Speedup_Stopwatch_Test_v1.2.rar

Please note that this tool has been reported for crashing the game, so don't just blame it on your hardware/software. Even though, it rarely does and only on some people.

Also, if you have Gentlemen of the Row, this is already included and configured in it so no need for this.

BIOS Method

This is, by far, the best method (or at least it is for me and many others who tried it). This method has only one problem: you have to edit your Motherboard's BIOS and have knowledge on how to do so. (Actually, that's not a problem.)

A big thanks goes to "EtaYorious", the defacto founder of this solution. By the way, this method is actually not too popular, YET ;)

All you have to do is turn "HPET" (High Precision Event Timer) and "ACPI" (Advanced Configuration and Power Interface) on. These settings depend on what kind of Motherboard you have, mostly the company that manufactured it.
ASUS for example, they have a specific name for ACPI, I can't remember. What I can remember though, is that there were three options, two of them were "Power On" and "Power Off". Choose "Power On" and you have ACPI on in an ASUS Motherboard.

For more information, most of the new motherboards already have HPET on, while ACPI is off.

Then, you'll have to use the Command Prompt to make sure it is enabled.

To do so, just press on start, then on the Search tab, type "cmd". A program named "cmd.exe" will appear.
Right click on it for its context menu, then click on "Run as Administrator".
In the CMD window, type "bcdedit /set useplatformclock true" without the quotes, then click enter and restart your PC.

One reader reported that by just using the CMD (no BIOS editing), he was able to fix Saints Row 2's speed. So I suggest for those that don't want to edit their BIOS to just do it with CMD, see if it will work just by this way.

Now, play Saints Row 2 and see if this worked for you.
REMEMBER: If you have PowerTools, you must remove it if you did the BIOS method.

Now, to test out if you have more/less speed than usual, all I can say is that you should go find some videos of Saints Row 2 being played on an Xbox. Then compare between Xbox and your own. This will surely not be so accurate, though, because of it being more about trial and error.

To make it a lot more accurate, you could get in Saints Row 2 and play a race minigame or any minigame that has a timer. If the timer goes faster/slower than usual, you know what's going on.

Perhaps the best way to test it is by using the Beta PowerTools Stopwatch feature. This will use an accurate Stopwatch to determine your speed and then automatically set the speed. (Though, like I said, it didn't work well for me)

So, as you already know thanks to this guide, there is no "Only one solution" but a variety of it. You are the one who finds the real solution.

Some people don't like PowerTools because it crashes their game, so they just use Cheat Engine.
Some don't like Cheat Engine because of the cutscene bug, so they use PowerTools.
As for the BIOS method, I'm not too sure, but I'm just gonna guess some don't like that method simply because you have to edit your BIOS and you're too worried you might screw up.

So, as I said before, you are the one who finds the solution.

Now, I'd like to give a big thanks to;

IdolNinja - he has dedicated his work on making SR2 (as well as the other ones) more playable, fun and stable, especially with Gentlemen of the Row. A big thanks goes to him and you all should thank him but not worship him, that is, don't add him as a Steam friend. He really hates that and I don't blame him.

Minimaul - he made PowerTools and other variety of useful tools for the Saints Row games. Without him, we'd be stuck using Cheat Engine.

EtaYorious - a big thanks to him simply because he found a great and simple solution for the Speedup bug.