Best way to store downloaded .exe files?

Over the last few months I have downloaded many...perhaps too many...free program files for download. Often times they are of the type .exe, sometimes they are .zip, sometimes .rar, and so on.

At first i was annoyed by compressed files because in a sense they were not ready to run. Gradually I realized two things that i think suggest that saving all the types as .rar is a safer way to save them

1) with RAR you can include a "recovery record" which can usually repair the file if it becomes corrupted.

2) And this is more of a question, if the downloaded file is malware, will RARing it prevent it from running as a trojan? would i need to use a password to extract them to get this hypothetical protection. And lastly, in practice will this make the programs safer, or is it just wasted effort on my part? Any thoughts on this?

- HandsOff