Not sure if you want (or care) about an opinion from Ohio, but here's my thoughts on the best west team ever. Please keep in mind the only time I saw any of these teams actually play was the Stagg Bowl, but here's my unwanted opinion anyway

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2003 SJU - only team to handle MUC in last 15+ years / Blake Elliott was by far the best player in D3 that year (and one of the best ever) and was The Difference in the Stagg that won it for SJU. In previous MUC/SJU games, MUC had the best individual player. Not in 2003. And it wasn't even close. All other spots are open to debate, but not #1. The following is just random thoughts (or lack thereof) and shouldn't be considered a listing in order.
The team I'm not sure where to rank is '05 WWW. From a pure
potential standpoint, I'd put the '05 WWW team way up the list. I'm stilll not sure how that team with such great size/speed defensively and offense diversity lost to a MUC team that was very young, inconsistent and hurt by significant injuries.
Production wise, I'd put them middle of the pack from losing to a decent MUC team but that contrasts their drilling of SJU and the win at Linfield. So I still don't know where to put them.
'04 Linfield is a "sexy" pick because of Brett Elliott at QB, but their showing against MHB in the Stagg was less than impressive in my eyes. MHB was a very solid team, but they weren't supposed to be competitive with Linfield. I also have a real hard to placing '04 Linfield above '05 WWW since they lost to them with the same team that won the championship in '04. I know each season is different, but a young '05 WWW team shouldn't go on the road to the defending and senior dominated Champs and win. That has to put WWW ahead of Linfield.
'99 PLU gets a bump from blasting Rowan in the Stagg, but KC Keeler and Company made a habit out of pissing down their leg in the Stagg. So I have a hard time believing that PLU was really that much better than the rest of D3 even though the Stagg was a blowout. Especially when you factor in that Keeler thought the only team in America that was a legit threat was MUC and forgot to show up in Salem, VA. No doubt PLU was a great team on a mission, but their Stagg win isn't anywhere close to SJU's Stagg win due to the opposing coach.
'06 WWW - on the plus side of the ledger, they returned everyone from '05 and was no longer in awe of being in the ESPN spotlight, played the season with the bullseye opposed to sneaking up on Linfield like '05, but was handled rather easily in the Stagg. Injury to Beaver mid-season should have made them better. Mitigating factor here is that the '06 MUC team was much, MUCH better than the '05 MUC team. So I'd put '06 WWW a spot or two ahead of '05 WWW, but still can't decide where to place them on the overall list.
'00 SJU - very good team that was well coached. Played an excellent game in Salem, but I came away from that game thinking that their best shot at MUC was that specific game. Which is the exact opposite of how I felt about the '05 WWW/MUC game as I kind of thought MUC stole one and probably wouldn't if they played again.
If I had to rank them, I'd go as such though I'm not real confident in anything past #1:
1. 2003 SJU
2. 2006 WWW
3. 2005 WWW
4. 2004 Linfield
5. 1999 PLU
6. 2000 SJU
I put WWW ahead of Linfield simply based on their win at Linfield in '05. If that game was a "lucky" win for WWW, then move Linfield to #2 and shift the two WWW teams to #3 and #4.