The difficulty in this is that there were very few parties that came close to winning seats but didn't IOTL.
The Greens didn't really come close in any particular constituency, just beat the Social and Liberal Democrats to third place and tallied a fair share of the vote nationally. Even after the advent of PR it seems most parties would need to already have some level of support to make a splash and the low turnout doesn't bode well for minor parties with such a limited number of seats per constituency up for grabs.
Some other possibilities...
Billy Fizz and Ken Clarke have a lager drinking contest sometime during the Conservative leadership election of 1997, and John Redwood wins. The Pro-Euro Conservative Party might win a seat or two in 1999.
More Labour MPs leaving the party over Iraq might lead to a Left List in 2004.
This is part of the reason why I asked the question - anyone who suggests the Greens winning a seat in 1989 is automatically going on my ignore list.
There were a couple of occasions where smaller parties got close to winning a seat, principally the BNP on various occasions. George Galloway wasn't too far off a seat in 2004, so a few different circumstances during the short campaign (or, as you say, a larger split) would get him in, which leads to a few interesting questions. I don't think he'd make much of an impact in Brussels, and he'd probably still embarrass himself on reality TV, but there's a greater chance that he doesn't personally contest Bethnal Green and Bow and, if he does, he may well lose. Now - if he wins, he is probably replaced in Brussels by the next guy on the List, Unjum Mirza, who was an SWP member. And if Respect is getting around 8% in the Euro elections in London, they're almost certainly getting more than 5% in the London Assembly elections on the same day. The first two people on the Assembly list just happened to be SWP members (although Oliur Rahman has had an... interesting political career). As one of the main reasons for the SWP split was that they weren't winning any seats out of the deal, the split is probably delayed - and you might just get an early Comrade Delta scenario bringing down Galloway as well as the SWP.
2004 also saw Martin Bell in the East of England and Steve Radford of the Liberals in the North West getting non-zero proportions of the vote, but I don't think either is terribly likely or terribly full of ramifications. Same for Christine Oddy (deselected Labour) in the West Midlands in 1999.
The other one I quite like is the possibility of the SSP in either 1999 or 2004 - especially 1999, as Hugh Kerr was
very English and pretty much detested by the rest of the party. You'd probably have more of an idea of the impacts of this than I do.