As a long time user of both, I can tell you that both have their pros and cons. It could take a long time to go over it in detail. Quickly:
iSiloPros:
- new version is very fast
- converter is clean and has an IE add-in
- works on Palm and PPC
- lots of ebooks available in this format
Cons:
- proprietary document format
- category system in latest version is counter-intuitive
- no add-in for Mozilla/Firefox
- little support for RSS feeds
- $20
PluckerPros:
- FREE!
- your choice of converter, basic python version, JPluck, or (brand new and recommended) Sunrise
- Mozilla/Firefox add-in
- good support of RSS
- lots more ebooks available in Plucker format
- open document format
- great category system
Cons:
- very little support on PPC (there's Vade Mecum, but it's pretty much dead)
- somewhat slower reader than iSilo (though not a big deal unless your PDA is slow)
- no add-in for IE
Can't think of anything else just now. Head over to
MobileRead.com for a lot more discussion of both readers and others. Each has its own forum and they are pretty active. I started out with iSilo and then moved over to Plucker. I think that I'll be moving back to iSilo soon, as I plan to get myself an x30 mid. Try them both.