Here is a step by step guide how to make version 1.98 portable (and probably later versions aswell).
1. Install clipdiary normally and run once;
2. Close by selecting File|Exit from menu (don't do escape or click window upper right x button, program will only minimize);
3. Find clipdiary install folder and copy it elsewhere (to USB drive, for example, if that's where you intend to run it);
4. In this folder created in step 3, make a new text file, name it clipdiary.bat and paste the following code into it.
rem Make local environment for variables;
rem Change the current directory to the location of the batch file;
rem Remember: Batch (.bat) file should reside in same folder as exe;
cd /d %~dp0
rem Create the required directory if it doesn't exists
if exist "Application Data" goto :aftermkdir
mkdir "Application Data"
rem Set the User Profile directory to the current location of the batchfile
@echo Launching ClipDiary...
@echo Your diary is stored in %USERPROFILE%Application Data\ClipDiary
rem Exit local environment;
5. Double click clipdiary.bat to start Clipdiary.
... And you're all set (again).