RegEx expression that will capture everything between two characters including multiline blocks

Which regex engine are you using?

<%(.*?)%>

should work with the "dot matches newline" option enabled. If you don't know how to set that, try

<%([\s\S]*?)%>

or

(?s)<%(.*?)%>

No need to escape <, %, or > by the way.

\<\%(.*?)\%\>. You need to use .*? to get non-greedy pattern matching.

EDIT To solve the multiline problem, you can't use the . wildcard, as it matches everything except newline. This option differs depending on your regular expressions engine. So, I can tell you what to do if you tell me your regex engine.

I've been using Microsoft's Regex engine (provided by JScript in IE) and it has a 'multi-line' switch that effects the behaviour of ., but then still I've had problems I had to resolve using [\u0000-\uFFFF] which matches everything including EOL's or any control chars...

So have a go with <%([\u0000-\uFFFF]*?)%>