I've started on a comparison page for PortableApps at http://cubegames.net/development/compare
From what I've been able to see, everything should be correct, but the page needs to be fleshed out with some better descriptions. The format is based on http://htmlpurifier.org/comparison.html
Anyone care to help out? 
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I tried to add to this using one of the 'Fix me' buttons, but no go. Here are some of the changes I propose:
U3
Developed by SanDisk and M-Systems, is included on some flash drives by various manufacturers. The software is based on making two partitions on the drive, with one configured to look like a CD-ROM and the other containing the user's data and applications. To remove the U3 software completely, you must use the vendor's software remover, which reformats the whole drive; it is not enough to delete the U3 launcher software. PortableApps applications can be used on a U3 drive, as can natively portable applications.
(add this as an alternative)
Moka5
Similar in functionality to MojoPac, Moka5 (http://www.mokafive.com) uses a portablized version of VMWare's Virtual Machine on an otherwise normal flash or other external drive. It shares some of the same advantages and disadvantages as VMWare. It requires a lot of memory, a higher performance CPU, and creates a separate contained environment with limited interaction with data and applications on the host computer.
The "Fix me" icons aren't buttons, unfortunately, you'll need to use the Edit page button (I've changed permissions for that page to allow anonymous editing).
I've added what you said onto the page. Can you verify what I've said about MokaFive and fill in the blanks please?
"If you're not part of the solution, you're part of the precipitate."
1. I suggest changing "PortableApps" to either "PortableApps.com apps" or "portable apps". That's misleading and I seriuosly don't know what do you mean.
2. "Allows any application" - not everything can be portabilized.
3. PortableApps security - in rare case of a crash or alike some app can break local computer. That's "very low". On the other hand some programs don't touch local machine at all, so I would write "varies".
But in general, ThinApp is WAY more secure.
4. "Works on user accounts" - The "yes" answer makes me think that you mean "PortableApps.com", right?
5. "Open API" - don you mean "has API with open documentation" or "has open source API"?
ThinApp has documented API.
6. MojoPac free edition has some limitations, you have to pay to use any app.
7. Are all PA.com apps Vista compatible? If so, I suggest updating their sites, i.e. Abi Word's one doesn't list it.
"Those people who think they know everything are a great annoyance to those of us who do." Asimov
"
2. "Allows any application" - not everything can be portabilized.
3. PortableApps security - in rare case of a crash or alike some app can break local computer. That's "very low". On the other hand some programs don't touch local machine at all, so I would write "varies".
"
I agree to both, and posted them yesterday on IRC
At #2 at this time I would say Security: none
"If you're not part of the solution, you're part of the precipitate."
4. This is not about stealthiness (or cleanness - I prefer this word).
PA.com apps can destroy (or at least make unaccessible) data on host computer. Destroying data is very insecure.
You should rename the entry to "password protection" or so.
Also, I think that you can use TC / OFTE with everything but U3, why do you mention it for PA.com only?
5. Thinstall lets you write scripts that are executed when certain things happen.
I.e. you can install a driver to the host machine on startup and uninstall it on close.
"Those people who think they know everything are a great annoyance to those of us who do." Asimov
It should be PortableApps.com. And U3 is far LESS popular than PortableApps.com. On an app to app basis we've always had 10 to 30 times the downloads.
Sometimes, the impossible can become possible, if you're awesome!
I agree that U3 is less popular than PortableApps.com, although I don't know why you mention it.
Please be aware that while PortableApps.com might be more popular, many people are aware of U3 because the USB sticks are sold in many, many shops. I bet that if you ask in shops that sell computer hardware most sales people will know what U3 is and not what PortableApps.com is. So the general public might be more aware of U3 than you think, and there still might be many, many U3 users, just because they don't know about PortableApps.com application.
It seems your assumption of popularity of those both formats is based on some articles and download statistics, while Joe the Plumber just has bought his U3 device and just uses it. (Yep many U3 devices are still being sold).
I hope in the future PortableApps.com will be more present in the consumer market where people buy their USB sticks. PEAK USB sticks are a good thing as they have little flyers actively promoting a few PortableApps.com products. I hope more and more support from the hardware part of the market will help raising awareness of PortableApps.com platform.
I swear I had "PortableApps.com". Fixed.
The popularity refers to number of installations on drives, rather than directly to downloads, as noted by LOGAN. It's also one of the most well-known systems. I've clarified this.
"If you're not part of the solution, you're part of the precipitate."
I love ya man, but it reads like an AD for portableapps.com
Security: Almost WITNOJTH !!! What you mean is NONE, but were working on something which even John calls "Security thru Obscurity"
Vista compatible: Yes ---> should be partial
Allows any application: Yes ---> If it ran any application we wouldn't be making apps would we ?
Price: U3 Depends on drive: That's just not fair really, You get a drive with it for pete's sake. And i have always been able to find U3 drives that are cheaper than non-u3's, so it is basically free.
Sorry, my friend, but objectivity is not showing here,
But i love you any way
Tim
Things have got to get better, they can't get worse, or can they?
Security is available with TrueCrypt, FreeOTFE, etc, which is why I put "Almost".
Every application is Vista compatible as per https://portableapps.com/apps/compatibility
I changed "Allows any application" to "Almost", as a lot of applications can be run through the PAT (or whatever it was called) and they will work. Compare this to U3, which basically only allows applications by the app author themselves. Also, any executable will appear on the menu, whereas it is a lot more work to have one appear on the U3 menu.
The price still depends on the drive regardless. The point here is that you can not buy U3 separately from a drive.
Feel free to edit the page yourself
"If you're not part of the solution, you're part of the precipitate."