1. Ease of use
   LinkFreeze is the unquestionable leader by this parameter. One dialog is everything you’ll deal with – all settings are set up there.
   

   ISAPI_Rewrite in its turn is far more complex tool – you need to be aware of (at least) the basics of regular expressions to manage it. Most of the configuration is stored in plain text files which may be edited in a special manager.

   
2. Functionality
   In this characteristic the situation is quite the contrary – ISAPI_Rewrite has incomparably more features than LinkFreeze, notably:
   – rewriting URLs in any way you want (e.g. having www.domain.com/seo_page-123.html refer to www.domain.com/real_page.aspx?param_id=123);
   – proxying (e.g. having www.external.com/any_page.html refer to www.internal.com/any_page.aspx);
   – mapfiles support (e.g. having www.domain.com/seo_page-param_name.html refer to www.domain.com/real_page.aspx?param_id=123);
   – filtering requests based on server variables’ values, IP addresses/domain names, referers, etc.LinkFreeze is achieving SEO-friendliness in a different way – it allows to make query string a part of the URL, move and change file extension (e.g. having www.domain.com/page_name-param_name-123.html refer to www.domain.com/page_name.aspx?param_name=123) but the wording of the URL remains intact (addition/replacement/deletion of URL portions is not possible).
3. SEO efficiency
   While LinkFreeze will automatically make your links on pages look like www.domain.com/page_name-param_name-123.html, with ISAPI_Rewrite3 you need to either alter them manually to look like www.domain.com/seo_page-param_name.html or use 301 redirects (this may slightly decrease the pagerank of the page) to SEO-friendly page names and reverse internal rewriting to the actual page name. Here’s how it looks like in terms of ISAPI_Rewrite 3 syntax:

   RewriteEngine on
   RewriteBase /
   RewriteCond %{QUERY_STRING} ^param_id=(\d+)$
   RewriteRule ^real_page\.aspx$ seo_page-%1.html? [NC,R=301,L]
   RewriteRule ^seo_page-(\d+)$ real_page.aspx?param_id=$1 [NC,L]

   So, the key difference is that LinkFreeze changes links on pages and ISAPI_Rewrite doesn’t!

4. Windows versions supported
   LinkFreeze supports Windows NT 4 (IIS 4), Windows 2000 (IIS 5), Windows XP (IIS 5.1) and Windows 2003 (IIS 6).ISAPI_Rewrite3 supports Windows 2000 (IIS 5), Windows XP (IIS 5.1), Windows 2003 (IIS 6), Windows Vista (IIS 7), Windows 2008 (IIS 7), Windows 7 (IIS 7.5) and Windows 2008 R2 (IIS 7.5).

   If you are the lucky user of IIS7 (7.5) and need ISAPI_Rewrite/LinkFreeze capabilities, you can benefit from using Helicon Ape tool which includes mod_rewrite and mod_linkfreeze as well as a bunch of other helpful modules and functions.

Hope this article favored better understanding of the products capabilities and peculiarities, and you choice will be more conscious.

Best regards,
Anton, Helicon Tech