Here is a small collection of tools I have written that may assist in the analysis of malware:

Labelmaster-olly-plugin.zip
Labelmaster is an OllyDbg plugin that can import/export user-defined labels and comments in batch. It's useful for transferring manual analysis from one file to another when editing or unpacking an EXE file. (The .udd file containing all your analysis work is tied to the CRC of the file you are examining).

upxrestore.pl
upxrestore.pl is a Perl script which can fix UPX headers that were removed by a hacked version of UPX used to pack certain malware.

olly2html.pl
olly2html.pl is a Perl script which creates cross-linked HTML pages from ASM generated by Ollydbg "Copy->File" function. You can view sample output of olly2html.pl (from an ASM dump of the Labelmaster plugin above) here.

OLE R-E Tools
This is a set of Perl scripts to assist in reverse-engineering OLE calls in executables.