What are the significant difference between them and which do you guys prefer?

I have never used prelude, as snort has been very good to me and I haven't found a reason to look elsewhere. Buy the Snort book from syngress and you can set up a mean IDS.

Your poll makes absolutely no sense. X vs Y? What are your grounds for this comparison? What makes one better than another? You can't just ask a question and not give us your own views.

I thought both perform the same task?

I'm just asking for opinions and recommendations before deciding which one to pick up.

Prelude also does HIDS if my recollection is correct. It has a little bit wider scope of coverage than Snort. On the other hand, Snort detects a lot more type of network attacks than Prelude does. It really depends on what you're trying to accomplish.

Prelude differs from Snort in that it uses a server-client (agent) setup. Prelude can do (or has hooks to) do more than be an (distributed) IDS agent: it can do filesystem integrity checking (like Aide, Samhain, Osiris, Integrit, tripwire) and IIRC rule-based policying (or interaction with) Niels Provos' Systrace. Both are similar in the fact they only do (mainly static) signature or rule-based matching (exaggerating), meaning there's no extensive built-in analysis and no decision logic to for instance automate the next step and (intelligently) correct or actively block traffic. Signature and rule-based also means in this respect that your detection capabilities are as strong as the rulesets and signatures you build. AFAIK products like Forestorm, Prelude etc etc are lagging behind compared to Snort when it comes to active community-based rule development (take a look on the snort-signatures mailinglist).

One of the things typically *NIX is to have one binary perform one task, and perform that task well. For reasons of widespread acceptance, large support community, active development, maturity, performance and the one taks thing I choose Snort anytime.